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
  • Structures With Same Primary Citation

  • 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 ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-AP206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-AQ232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15E117Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2R216Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3A222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5B206Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-AT228Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-AU184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8V187Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for A0A0J9X221 (Lachancea kluyveri)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-AW184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-AC92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-AX142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12D121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13Y150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-BZ127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
Find proteins for P39516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-AF141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-BG125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17BRP51BYDR447C
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-AH145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-AI143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-Aa87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-Ab129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-Ad134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-AK82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-Be97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-Af81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-AM53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-Ag60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31N73Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like proteinO312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-AL63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1-ABT204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1ASSM1SSM1AYPL220W
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AAW251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3BA386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-ABE361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5BI294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-ABO222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AAA233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10BD218Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-BAG169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AAJ193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AAM136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AAQ203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AAU197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AAX183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-ABB185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-ABF188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-ABH171Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-ABJ159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-ABL100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AAB136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-AAE126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25AH121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-AAK125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-AAN135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28AR148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29AV58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30AY96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-ABC109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32BG127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-ABK106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-ABN112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-ABP119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-AAC99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-AAF81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39AL50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40AO52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-BAS25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41BRPL47BYL41BYDL133C-AYDL133BC
Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AAP103Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AAT91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-ABV22Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
General negative regulator of transcription subunit 5BW112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOT5YPR072WYP9499.27
Find proteins for Q12514 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20J100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-Ac144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-BBM175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6BRPL16BRPL17BYL16BYLR448WL9324.4
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AAD191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38AI77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-AS258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 18S ribosomal RNA (RDN18-1), rRNA21798Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChainsLengthOrganism
mRNAl3Saccharomyces cerevisiae S288C

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Entity ID: 24
MoleculeChainsLengthOrganism
tRNAn75Saccharomyces cerevisiae S288C

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Entity ID: 37
MoleculeChainsLengthOrganism
25S rRNABQ3223Saccharomyces cerevisiae S288C

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Entity ID: 39
MoleculeChainsLengthOrganism
5S rRNABR121Saccharomyces cerevisiae S288C

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Entity ID: 40
MoleculeChainsLengthOrganism
5.8S rRNABS158Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPD
Query on SPD

Download CCD File 
BQ
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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AF, AO, AP, AT, BN, M, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download 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



Entry History & Funding Information

Deposition Data


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

Revision History 

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