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: 3.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 

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.

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

(2016) EMBO Rep 17: 1776-1784

  • DOI: 10.15252/embr.201642943
  • Structures With Same Primary Citation

  • 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

    Strasbourg University, Strasbourg, France.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-A
S0, s0
206Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for B3LI22 (Saccharomyces cerevisiae (strain RM11-1a))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-A
S1, s1
216Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for B3RHV0 (Saccharomyces cerevisiae (strain RM11-1a))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2
S2, s2
217Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3
S3, s3
223Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-A
S4, s4
260Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5
S5, s5
206Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-A
S6, s6
226Saccharomyces cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
S8, s8
188Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for A0A0J9X221 (Lachancea kluyveri)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-A
S9, s9
185Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A,40S Ribosomal Protein S10
C0
96Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-A,40S Ribosomal Protein S11
C1, c1
155Saccharomyces cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S Ribosomal Protein S15,40S ribosomal protein S15,40S Ribosomal Protein S15
C5, c5
135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-A
C6, c6
142Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-A
C8, c8
145Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-A
C9, c9
143Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20
D0, d0
110Saccharomyces cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-A
D3, d3
144Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CY39 (Naumovozyma castellii (strain ATCC 76901 / CBS 4309 / NBRC 1992 / NRRL Y-12630))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-A
D5, d5
70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-B
D6, d6
97Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-A
D7, d7
81Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-A
D8, d8
63Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-A
D9, d9
53Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-A
E0, e0
62Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31
E1, e1
76Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
SR
318Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Ribosome-bound protein Stm1,Suppressor protein STM1,Ribosome-bound protein Stm1
SM
159Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
L2, l2
252Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
L3, l3
386Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
L4, l4
361Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
L5, l5
296Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
L6, l6
175Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
L7, l7
223Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
L8
233Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
M0, m0
220Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
M1, m1
169Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E757

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
M3, m3
194Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
M4, m4
137Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
M5, m5
203Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
M6, m6
197Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
M7, m7
183Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
M8, m8
185Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
M9, m9
188Saccharomyces cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
N3, n3
136Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
N5, n5
121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
N7, n7
135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
N8, n8
148Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
N9, n9
58Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
O0, o0
100Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
O1, o1
109Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
O2, o2
127Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
O3, o3
106Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
O4, o4
112Saccharomyces cerevisiaeMutation(s): 0 
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 cerevisiaeMutation(s): 0 
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
O6, o6
99Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
O7, o7
87Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
O8, o8
77Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
O9, o9
50Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
Q0, q0
52Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
Q1, q1
25Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
Q2, q2
105Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
Q3, q3
91Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-A,40S Ribosomal Protein S10
c0
96Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like protein
sR
318Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 86
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A,60S Ribosomal Protein L8
l8
231Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 87
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein L12
m2
150Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 88
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
n4
135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 89
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein P0
p0
143Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 90
MoleculeChainsSequence LengthOrganismDetails
60S Ribosomal Protein P1/2
p1, p2
47Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ES17
C7
120Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for A0A0J9X224 (Lachancea kluyveri)
Go to UniProtKB:  A0A0J9X224

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-A
D2, d2
129Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-A
D4, d4
134Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
L9, l9
191Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
N4
98Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
N6, n6
126Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
ES17
c7
121Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for A0A0J9X224 (Lachancea kluyveri)
Go to UniProtKB:  A0A0J9X224

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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STM1,Ribosome-bound protein Stm1
sM
104Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P39015

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Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA21812Saccharomyces cerevisiae

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Entity ID: 36
MoleculeChainsLengthOrganism
25S ribosomal RNA13149Saccharomyces cerevisiae

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Entity ID: 37
MoleculeChainsLengthOrganism
5S ribosomal RNA3, 7121Saccharomyces cerevisiae

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Entity ID: 38
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4, 8158Saccharomyces cerevisiae

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Entity ID: 80
MoleculeChainsLengthOrganism
18S ribosomal RNA61800Saccharomyces cerevisiae

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Entity ID: 85
MoleculeChainsLengthOrganism
25S ribosomal RNA53150Saccharomyces cerevisiae
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Entity ID: 91
MoleculeChainsLengthOrganism
Peptidyl-tRNA analog ACCA-Leu-PheP, p5Homo sapiens
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPS
Query on SPS

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1, 5
SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
 Ligand Interaction
8AN
Query on 8AN

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

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

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1, 5
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
LEU
Query on LEU

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1, 5
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.262 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 434.73α = 90
b = 286.77β = 98.87
c = 303.15γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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