5IT9

Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of ribosome recruitment and translocation by type IV IRES.

Murray, J.Savva, C.G.Shin, B.S.Dever, T.E.Ramakrishnan, V.Fernandez, I.S.

(2016) Elife 5

  • DOI: 10.7554/eLife.13567
  • Primary Citation of Related Structures:  
    5IT9, 5IT7

  • PubMed Abstract: 
  • Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs ...

    Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS2A206Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS1B214Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS5C217Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CKL3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS3D223Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS4E260Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS7F206Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS6G226Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS7H184Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CTD6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 9
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Ribosomal protein eS8I200Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS4J182Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CM18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 11
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Ribosomal protein eS10K96Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS17L155Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS12M122Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS15N150Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 15
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Ribosomal protein uS14O127Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 16
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Ribosomal protein uS19P123Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CKV4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 17
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Ribosomal protein uS9Q141Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS17R129Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS13S145Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS19T143Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS10U106Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CIM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS21V87Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS8W129Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein uS21X145Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q875M3 (Kluyveromyces lactis)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS24Y134Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS25Z70Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CW78 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS26AA [auth a]100Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein eS27BA [auth b]82Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 29
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Ribosomal protein eS28CA [auth c]63Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 30
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Ribosomal protein eS29DA [auth d]53Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 31
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Ribosomal protein eS30EA [auth e]55Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 32
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Ribosomal protein eS31FA [auth f]69Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 33
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Ribosomal protein RACK1GA [auth g]324Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S ribosomal RNAHA [auth 2]1780Kluyveromyces lactis
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Entity ID: 35
MoleculeChainsLengthOrganismImage
Cricket paralysis virus IRES RNAIA [auth i]192Cricket paralysis virus
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
NA [auth a], OA [auth b], PA [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2] , AC [auth 2] , AD [auth 2] , BB [auth 2] , BC [auth 2] , BD [auth 2] , CB [auth 2] , CC [auth 2] , 
AB [auth 2],  AC [auth 2],  AD [auth 2],  BB [auth 2],  BC [auth 2],  BD [auth 2],  CB [auth 2],  CC [auth 2],  CD [auth 2],  DB [auth 2],  DC [auth 2],  DD [auth 2],  EB [auth 2],  EC [auth 2],  ED [auth 2],  FB [auth 2],  FC [auth 2],  FD [auth 2],  GB [auth 2],  GC [auth 2],  GD [auth 2],  HB [auth 2],  HC [auth 2],  HD [auth 2],  IB [auth 2],  IC [auth 2],  ID [auth 2],  JA [auth G],  JB [auth 2],  JC [auth 2],  JD [auth 2],  KA [auth N],  KB [auth 2],  KC [auth 2],  KD [auth 2],  LA [auth T],  LB [auth 2],  LC [auth 2],  LD [auth 2],  MA [auth X],  MB [auth 2],  MC [auth 2],  MD [auth 2],  NB [auth 2],  NC [auth 2],  ND [auth 2],  OB [auth 2],  OC [auth 2],  PB [auth 2],  PC [auth 2],  QA [auth 2],  QB [auth 2],  QC [auth 2],  RA [auth 2],  RB [auth 2],  RC [auth 2],  SA [auth 2],  SB [auth 2],  SC [auth 2],  TA [auth 2],  TB [auth 2],  TC [auth 2],  UA [auth 2],  UB [auth 2],  UC [auth 2],  VA [auth 2],  VB [auth 2],  VC [auth 2],  WA [auth 2],  WB [auth 2],  WC [auth 2],  XA [auth 2],  XB [auth 2],  XC [auth 2],  YA [auth 2],  YB [auth 2],  YC [auth 2],  ZA [auth 2],  ZB [auth 2],  ZC [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
National Institutes of HealthUnited StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.2: 2019-12-11
    Changes: Advisory, Derived calculations, Other