6TB3

yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The Ccr4-Not complex monitors the translating ribosome for codon optimality.

Buschauer, R., Matsuo, Y., Sugiyama, T., Chen, Y.H., Alhusaini, N., Sweet, T., Ikeuchi, K., Cheng, J., Matsuki, Y., Nobuta, R., Gilmozzi, A., Berninghausen, O., Tesina, P., Becker, T., Coller, J., Inada, T., Beckmann, R.

(2020) Science 368

  • DOI: 10.1126/science.aay6912
  • Primary Citation of Related Structures:  
    6TNU, 6TB3

  • PubMed Abstract: 

    • Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality ...

    Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability.

    Organizational Affiliation: 

    Gene Center and Department of Biochemistry, University of Munich, 81377 Munich, Germany. beckmann@genzentrum.lmu.de toshifumi.inada.a3@tohoku.ac.jp jmc71@case.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-A P206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32905 
Go to UniProtKB:  P32905
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-A Q232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33442 
Go to UniProtKB:  P33442
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15 E117Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15, RPS21, YOL040C
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01855 
Go to UniProtKB:  Q01855
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2 R216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25443 
Go to UniProtKB:  P25443
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3 A222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05750 
Go to UniProtKB:  P05750
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-A S258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX35 
Go to UniProtKB:  P0CX35
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5 B206Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-A T228Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX37 
Go to UniProtKB:  P0CX37
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-A U184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26786 
Go to UniProtKB:  P26786
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S8 V187Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for A0A0J9X221 (Lachancea kluyveri)
Explore A0A0J9X221 
Go to UniProtKB:  A0A0J9X221
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S9-A W184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore O13516 
Go to UniProtKB:  O13516
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10-A C92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10A, YOR293W
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08745 
Go to UniProtKB:  Q08745
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11-A X142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX47 
Go to UniProtKB:  P0CX47
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12 D121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48589 
Go to UniProtKB:  P48589
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13 Y150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05756 
Go to UniProtKB:  P05756
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14-B Z127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14B, CRY2, YJL191W, J0354
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39516 
Go to UniProtKB:  P39516
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16-A F141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX51 
Go to UniProtKB:  P0CX51
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17-B G125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17B, RP51B, YDR447C
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14127 
Go to UniProtKB:  P14127
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18-A H145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX55 
Go to UniProtKB:  P0CX55
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19-A I143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19A, RP55A, RPS16AA, YOL121C
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07280 
Go to UniProtKB:  P07280
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20 J100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20, URP2, YHL015W
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38701 
Go to UniProtKB:  P38701
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21-A a87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0V8 
Go to UniProtKB:  P0C0V8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22-A b129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C0W1 
Go to UniProtKB:  P0C0W1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-A c144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX29 
Go to UniProtKB:  P0CX29
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24-A d134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX31 
Go to UniProtKB:  P0CX31
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S25-A K82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25A, RPS31A, YGR027C
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E792 
Go to UniProtKB:  Q3E792
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-B e97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26B, YER131W
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39939 
Go to UniProtKB:  P39939
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27-A f81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35997 
Go to UniProtKB:  P35997
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S29-A M53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29A, RPS36A, YS29A, YLR388W, L8084.11
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41057 
Go to UniProtKB:  P41057
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S30-A g60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX33 
Go to UniProtKB:  P0CX33
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31 N73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05759 
Go to UniProtKB:  P05759
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like protein O312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1, CPC2, YMR116C, YM9718.15C
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38011 
Go to UniProtKB:  P38011
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-A L63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E7X9 
Go to UniProtKB:  Q3E7X9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L1-A BT204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1A, SSM1, SSM1A, YPL220W
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX43 
Go to UniProtKB:  P0CX43
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L2-A AW251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX45 
Go to UniProtKB:  P0CX45
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L3 BA386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14126 
Go to UniProtKB:  P14126
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L4-A BE361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10664 
Go to UniProtKB:  P10664
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L5 BI294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26321 
Go to UniProtKB:  P26321
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L6-B BM175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6B, RPL16B, RPL17B, YL16B, YLR448W, L9324.4
Find proteins for P05739 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05739 
Go to UniProtKB:  P05739
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L7-A BO222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05737 
Go to UniProtKB:  P05737
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L8-A AA233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17076 
Go to UniProtKB:  P17076
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L9-A AD191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05738 
Go to UniProtKB:  P05738
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L10 BD218Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10, GRC5, QSR1, YLR075W
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41805 
Go to UniProtKB:  P41805
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L11-B AG169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11B, RP39B, RPL16B, YGR085C
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E757 
Go to UniProtKB:  Q3E757
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L13-A AJ193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12690 
Go to UniProtKB:  Q12690
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L14-A AM136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36105 
Go to UniProtKB:  P36105
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L15-A AQ203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05748 
Go to UniProtKB:  P05748
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L16-A AU197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P26784 
Go to UniProtKB:  P26784
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L17-A AX183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05740 
Go to UniProtKB:  P05740
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-A BB185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX49 
Go to UniProtKB:  P0CX49
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L19-A BF188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX82 
Go to UniProtKB:  P0CX82
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L20-A BH171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX23 
Go to UniProtKB:  P0CX23
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-A BJ159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02753 
Go to UniProtKB:  Q02753
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L22-A BL100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05749 
Go to UniProtKB:  P05749
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L23-A AB136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX41 
Go to UniProtKB:  P0CX41
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24-A AE126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24A, RP29, RPL30A, YGL031C
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04449 
Go to UniProtKB:  P04449
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25 AH121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04456 
Go to UniProtKB:  P04456
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L26-A AK125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05743 
Go to UniProtKB:  P05743
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L27-A AN135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H6 
Go to UniProtKB:  P0C2H6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28 AR148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02406 
Go to UniProtKB:  P02406
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29 AV58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29, YL43, YFR032C-A, YFR032BW
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05747 
Go to UniProtKB:  P05747
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30 AY96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14120 
Go to UniProtKB:  P14120
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-A BC109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0C2H8 
Go to UniProtKB:  P0C2H8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32 BG127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38061 
Go to UniProtKB:  P38061
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-A BK106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05744 
Go to UniProtKB:  P05744
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-A BN112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P87262 
Go to UniProtKB:  P87262
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-A BP119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX84 
Go to UniProtKB:  P0CX84
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-A AC99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05745 
Go to UniProtKB:  P05745
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-A AF81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49166 
Go to UniProtKB:  P49166
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38 AI77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49167 
Go to UniProtKB:  P49167
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39 AL50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04650 
Go to UniProtKB:  P04650
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40 AO52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CH08 
Go to UniProtKB:  P0CH08
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-B AS25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41B, RPL47B, YL41B, YDL133C-A, YDL133BC
Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX87 
Go to UniProtKB:  P0CX87
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-A AP103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42A, RPL41A, SCL41A, YNL162W, N1722
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX27 
Go to UniProtKB:  P0CX27
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-A AT91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX25 
Go to UniProtKB:  P0CX25
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-A BV22Saccharomyces cerevisiae S288CMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetailsImage
General negative regulator of transcription subunit 5 BW112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOT5, YPR072W, YP9499.27
Find proteins for Q12514 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12514 
Go to UniProtKB:  Q12514
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA21798Saccharomyces cerevisiae S288C
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    mRNAl3Saccharomyces cerevisiae S288C
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    tRNAn75Saccharomyces cerevisiae S288C
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 37
    MoleculeChainsLengthOrganismImage
    25S rRNABQ3223Saccharomyces cerevisiae S288C
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 39
    MoleculeChainsLengthOrganismImage
    5S rRNABR121Saccharomyces cerevisiae S288C
    Find similar nucleic acids by: 
    (by identity cutoff)  |  Structure
    Entity ID: 40
    MoleculeChainsLengthOrganismImage
    5.8S rRNABS158Saccharomyces cerevisiae S288C
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SPD
    Query on SPD
    Download Ideal Coordinates CCD File 
    BQ
    		SPERMIDINE
    C7 H19 N3
    ATHGHQPFGPMSJY-UHFFFAOYSA-N    		 Ligand Interaction
    ZN
    Query on ZN
    Download Ideal Coordinates CCD File 
    AF, AO, AP, AT, BN, M, N
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    MG
    Query on MG
    Download Ideal Coordinates CCD File 
    2, AB, AQ, AW, AX, B, BA, BF, BG, BN, BO, BQ, BR, S, n
    		MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.80 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    German Research Foundation (DFG)GermanyBE1814/15-1

    Revision History  (Full details and data files)

    • Version 1.0: 2020-04-22
      Type: Initial release
    • Version 1.1: 2020-04-29
      Changes: Database references