5TGM

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCA-Pro


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular insights into protein synthesis with proline residues.

Mailliot, J.Rigger, L.Neuner, S.Shin, B.S.Yusupova, G.Dever, T.E.Micura, R.Yusupov, M.Melnikov, S.

(2016) EMBO Rep. 17: 1776-1784

  • DOI: 10.15252/embr.201642943
  • Primary Citation of Related Structures:  5LYB, 5TGA

  • PubMed Abstract: 
  • Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with oth ...

    Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs. These structures provide a high-resolution insight into unique properties of proline as a ribosome substrate. They show that the cyclic structure of proline residue prevents proline positioning in the amino acid binding pocket and affects the nascent peptide chain position in the ribosomal peptide exit tunnel. These observations extend current knowledge of the protein synthesis mechanism. They also revise an old dogma that amino acids bind the ribosomal active site in a uniform way by showing that proline has a binding mode distinct from other amino acids.


    Organizational Affiliation

    Institute of Genetics and Molecular and Cellular Biology CNRS UMR7104 INSERM UMR964, Illkirch, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
S0, s0
206Saccharomyces cerevisiae (strain RM11-1a)Gene Names: RPS0A (NAB1, NAB1A, YST1)
Find proteins for B3LI22 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3LI22
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
S1, s1
216Saccharomyces cerevisiae (strain RM11-1a)Gene Names: RPS1A
Find proteins for B3RHV0 (Saccharomyces cerevisiae (strain RM11-1a))
Go to UniProtKB:  B3RHV0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
S2, s2
217Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS2 (RPS4, SUP38, SUP44)
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25443
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
S3, s3
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS3 (SUF14)
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P05750
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S4, s4
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS4A (RPS7B)
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX35
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
S5, s5
206Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS5 (RPS2)
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P26783
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
S6, s6
226Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS6A (RPS101, RPS10B)
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-A
S7, s7
186Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS7A (RPS30)
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26786
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
S8, s8
188Lachancea kluyveriN/A
Find proteins for A0A0J9X221 (Lachancea kluyveri)
Go to UniProtKB:  A0A0J9X221
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
S9, s9
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS9A (RPS13A, YS11A)
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  O13516
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A,40S Ribosomal Protein S10
C0
96Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08745
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A,40S Ribosomal Protein S11
C1, c1
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS11A (RPS18A)
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S12,40S ribosomal protein S12
C2, c2
124Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS12
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13
C3, c3
150Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS13 (RPS13C)
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-A
C4, c4
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS14A (CRY1, RPL59)
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P06367
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
C5, c5
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS15 (RPS21)
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPS15
Go to UniProtKB:  Q01855
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
C6, c6
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS16A (RP61R)
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX51
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ES17
C7
120Lachancea kluyveriN/A
Find proteins for A0A0J9X224 (Lachancea kluyveri)
Go to UniProtKB:  A0A0J9X224
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
C8, c8
145Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS18A
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX55
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
C9, c9
143Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS19A (RP55A, RPS16AA)
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07280
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
D0, d0
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS20 (URP2)
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-A
D1, d1
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS21A (RPS25, RPS25A, RPS26A)
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
D2, d2
129Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS22A (RPS24, RPS24A)
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W1
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
D3, d3
144Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630)Gene Names: RPS23A
Find proteins for P0CY39 (Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630))
Go to UniProtKB:  P0CY39
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
D4, d4
134Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS24A (RPS24EA)
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX31
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
D5, d5
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS25A (RPS31A)
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E792
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
D6, d6
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS26B
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39939
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
D7, d7
81Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS27A
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P35997
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
D8, d8
63Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS28A (RPS33, RPS33A)
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E7X9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
D9, d9
53Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS29A (RPS36A, YS29A)
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41057
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
E0, e0
62Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS30A
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX33
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
E1, e1
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS31 (RPS37, UBI3)
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05759
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
SR
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38011
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1
SM
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39015
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
L2, l2
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
L3, l3
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL3
Go to UniProtKB:  P14126
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
L4, l4
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
L5, l5
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
L6, l6
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
L7, l7
223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
L8
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
L9, l9
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
M0, m0
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
M1, m1
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E757
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
M3, m3
194Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12690
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M4, m4
137Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
M5, m5
203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
M6, m6
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
M7, m7
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
M8, m8
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
M9, m9
188Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
N0, n0
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
N1, n1
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
N2, n2
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
N3, n3
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
N4
98Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
N5, n5
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
N6, n6
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
N7, n7
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
N8, n8
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P02406
Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
N9, n9
58Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL29
Go to UniProtKB:  P05747
Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
O0, o0
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P14120
Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
O1, o1
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
O2, o2
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38061
Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
O3, o3
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
O4, o4
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
O5, o5
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
O6, o6
99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
O7, o7
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
O8, o8
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
O9, o9
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
Q0, q0
52Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
Q1, q1
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX86
Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
Q2, q2
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
Q3, q3
91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A,40S Ribosomal Protein S10
c0
96Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPS10A
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08745
Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
ES17
c7
121Lachancea kluyveriN/A
Find proteins for A0A0J9X224 (Lachancea kluyveri)
Go to UniProtKB:  A0A0J9X224
Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
sR
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ASC1 (CPC2)
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38011
Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STM1,Ribosome-bound protein Stm1
sM
104Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: STM1 (MPT4, STO1)
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39015
Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A,60S Ribosomal Protein L8
l8
231Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein L12
m2
150N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 88
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
n4
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 89
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein P0
p0
143N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 90
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein P1/2
p1, p2
47N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA21812Saccharomyces cerevisiae
Entity ID: 36
MoleculeChainsLengthOrganism
25S ribosomal RNA13149Saccharomyces cerevisiae
Entity ID: 37
MoleculeChainsLengthOrganism
5S ribosomal RNA3,7121Saccharomyces cerevisiae
Entity ID: 38
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4,8158Saccharomyces cerevisiae
Entity ID: 80
MoleculeChainsLengthOrganism
18S ribosomal RNA61800Saccharomyces cerevisiae
Entity ID: 85
MoleculeChainsLengthOrganism
25S ribosomal RNA53150Saccharomyces cerevisiae
Entity ID: 91
MoleculeChainsLengthOrganism
Peptidyl-tRNA analog ACCA-Leu-PheP,p5Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
d6, D6, D7, d7, D9, d9, E1, e1, O7, o7, Q0, q0, q2, Q2, Q3, q3
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

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Download CCD File 
1, 5
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
OHX
Query on OHX

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Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, c3, C3, c5, C5, C7, C8, c8, d4, D9, l3, L3, L4, l5, L6, l9, M0, m0, m5, M5, m6, M6, M7, M8, m8, M9, m9, n9, N9, o3, O3, O4, O7, o7, O9, Q2, q2, s1, s4, s8, S8, S9, s9, SR, sR
osmium (III) hexammine
osmium(6+) hexaazanide
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
 Ligand Interaction
PHE
Query on PHE

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Download CCD File 
1, 5
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, C1, c6, C8, c8, C9, c9, d3, d4, d6, d7, D9, l2, L2, L3, l3, L4, l5, l6, l7, L7, l9, M0, m0, M3, m4, M5, m5, m6, m7, M7, N0, n0, n3, N3, N5, N6, n6, n8, N8, n9, o2, o3, O4, o4, O5, O7, o9, p, P, q1, Q2, s4, S4, s6, sM
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
8AN
Query on 8AN

Download SDF File 
Download CCD File 
P, p
3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
C10 H15 N6 O6 P
WIVGZDLLXCRANL-QYYRPYCUSA-N
 Ligand Interaction
SPS
Query on SPS

Download SDF File 
Download CCD File 
1, 5
SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NA
Query on NA
P, p
NON-POLYMERNa

--

UNK
Query on UNK
C0, c0, C1, c1, c2, C2, C5, c5, l8, m2, p, P, p0, p1, p2, sM, SM
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 434.730α = 90.00
b = 286.770β = 98.87
c = 303.150γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXphasing
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Derived calculations, Source and taxonomy, Structure summary