5TGA

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: 3.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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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
  • Primary Citation of Related Structures:  
    5LYB, 5TGA, 5TGM

  • 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 other amino acids both as a donor and as an acceptor of the nascent peptide ...

    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.



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Entity ID: 2
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40S ribosomal protein S0-AB [auth S0], CC [auth s0]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AC [auth S1], DC [auth s1]216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2D [auth S2], EC [auth s2]217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3E [auth S3], FC [auth s3]223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AF [auth S4], GC [auth s4]260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5G [auth S5], HC [auth s5]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AH [auth S6], IC [auth s6]226Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AI [auth S7], JC [auth s7]186Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AJ [auth S8], KC [auth s8]199Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-AK [auth S9], LC [auth s9]185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-AL [auth C0]96Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AM [auth C1], NC [auth c1]155Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12N [auth C2], OC [auth c2]124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13O [auth C3], PC [auth c3]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-BP [auth C4], QC [auth c4]128Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15Q [auth C5], RC [auth c5]135Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AR [auth C6], SC [auth c6]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-BS [auth C7], TC [auth c7]125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AT [auth C8], UC [auth c8]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-AU [auth C9], VC [auth c9]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20V [auth D0], WC [auth d0]110Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-AW [auth D1], XC [auth d1]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AX [auth D2], YC [auth d2]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-AY [auth D3], ZC [auth d3]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AZ [auth D4], AD [auth d4]134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-AAA [auth D5], BD [auth d5]70Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-BBA [auth D6], CD [auth d6]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ACA [auth D7], DD [auth d7]81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-ADA [auth D8], ED [auth d8]63Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-AEA [auth D9], FD [auth d9]53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AFA [auth E0], GD [auth e0]62Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31GA [auth E1], HD [auth e1]76Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinHA [auth SR], ID [auth sR]318Saccharomyces cerevisiaeMutation(s): 0 
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Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound protein Stm1IA [auth SM]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-AMA [auth L2], ND [auth l2]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3NA [auth L3], OD [auth l3]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AOA [auth L4], PD [auth l4]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5PA [auth L5], QD [auth l5]296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AQA [auth L6], RD [auth l6]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-ARA [auth L7], SD [auth l7]223Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-ASA [auth L8], TD [auth l8]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-ATA [auth L9], UD [auth l9]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10UA [auth M0], VD [auth m0]220Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BVA [auth M1], WD [auth m1]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AWA [auth M3], YD [auth m3]194Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AXA [auth M4], ZD [auth m4]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AYA [auth M5], AE [auth m5]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AZA [auth M6], BE [auth m6]197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AAB [auth M7], CE [auth m7]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-ABB [auth M8], DE [auth m8]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-ACB [auth M9], EE [auth m9]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-ADB [auth N0], FE [auth n0]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AEB [auth N1], GE [auth n1]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AFB [auth N2], HE [auth n2]100Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AGB [auth N3], IE [auth n3]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AHB [auth N4], JE [auth n4]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25IB [auth N5], KE [auth n5]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L26-AJB [auth N6], LE [auth n6]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S ribosomal protein L27-AKB [auth N7], ME [auth n7]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S ribosomal protein L28LB [auth N8], NE [auth n8]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S ribosomal protein L29MB [auth N9], OE [auth n9]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L30NB [auth O0], PE [auth o0]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L31-AOB [auth O1], QE [auth o1]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L32PB [auth O2], RE [auth o2]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L33-AQB [auth O3], SE [auth o3]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L34-ARB [auth O4], TE [auth o4]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L35-ASB [auth O5], UE [auth o5]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L36-ATB [auth O6], VE [auth o6]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L37-AUB [auth O7], WE [auth o7]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L38VB [auth O8], XE [auth o8]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L39WB [auth O9], YE [auth o9]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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Ubiquitin-60S ribosomal protein L40XB [auth Q0], ZE [auth q0]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L41-AYB [auth Q1], AF [auth q1]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L42-AZB [auth Q2], BF [auth q2]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L43-AAC [auth Q3], CF [auth q3]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10-AMC [auth c0]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound protein Stm1JD [auth sM]104Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
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60S Ribosomal Protein L12XD [auth m2]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 84
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60S acidic ribosomal protein P0DF [auth p0]219Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 85
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60S Ribosomal Protein P1/2EF [auth p1], FF [auth p2]47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNAA [auth 2]1829Saccharomyces cerevisiae
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Entity ID: 36
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25S ribosomal RNAJA [auth 1], KD [auth 5]3394Saccharomyces cerevisiae
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Entity ID: 37
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5S ribosomal RNAKA [auth 3], LD [auth 7]121Saccharomyces cerevisiae
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Entity ID: 38
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5.8S ribosomal RNALA [auth 4], MD [auth 8]158Saccharomyces cerevisiae
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Entity ID: 80
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18S ribosomal RNABC [auth 6]1800Saccharomyces cerevisiae
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8AN (Subject of Investigation/LOI)
Query on 8AN

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HU [auth 1], XKC [auth 5]3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
C10 H15 N6 O6 P
WIVGZDLLXCRANL-QYYRPYCUSA-N
 Ligand Interaction
C (Subject of Investigation/LOI)
Query on C

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FU [auth 1], GU [auth 1], VKC [auth 5], WKC [auth 5]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
 Ligand Interaction
OHX (Subject of Investigation/LOI)
Query on OHX

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