5IT7

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    5IT7, 5IT9

  • 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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D16027pD [auth AA]249Kluyveromyces lactisMutation(s): 0 
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Entity ID: 5
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60S ribosomal protein L3E [auth BB]384Kluyveromyces lactisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B07139pF [auth CC]360Kluyveromyces lactisMutation(s): 0 
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Find proteins for Q6CW41 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 7
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KLLA0D06941pG [auth DD]295Kluyveromyces lactisMutation(s): 0 
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Entity ID: 8
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KLLA0B04686pH [auth EE]170Kluyveromyces lactisMutation(s): 0 
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KLLA0D03410pI [auth FF]222Kluyveromyces lactisMutation(s): 0 
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KLLA0E00573pJ [auth GG]233Kluyveromyces lactisMutation(s): 0 
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KLLA0F04499pK [auth HH]191Kluyveromyces lactisMutation(s): 0 
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KLLA0D05643pL [auth II]216Kluyveromyces lactisMutation(s): 0 
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KLLA0F08261pM [auth JJ]168Kluyveromyces lactisMutation(s): 0 
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Entity ID: 14
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60S ribosomal protein L13N [auth LL]197Kluyveromyces lactisMutation(s): 0 
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KLLA0B13409pO [auth MM]136Kluyveromyces lactisMutation(s): 0 
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Ribosomal protein L15P [auth NN]202Kluyveromyces lactisMutation(s): 0 
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KLLA0F04675pQ [auth OO]198Kluyveromyces lactisMutation(s): 0 
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KLLA0A06336pR [auth PP]180Kluyveromyces lactisMutation(s): 0 
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KLLA0A07227pS [auth QQ]184Kluyveromyces lactisMutation(s): 0 
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KLLA0E12453pT [auth RR]188Kluyveromyces lactisMutation(s): 0 
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60S ribosomal protein L20U [auth SS]169Kluyveromyces lactisMutation(s): 0 
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KLLA0E23651pV [auth TT]158Kluyveromyces lactisMutation(s): 0 
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Entity ID: 23
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KLLA0D05181pW [auth UU]100Kluyveromyces lactisMutation(s): 0 
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KLLA0E06997pX [auth VV]132Kluyveromyces lactisMutation(s): 0 
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60S ribosomal protein L24Y [auth WW]62Kluyveromyces lactisMutation(s): 0 
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Find proteins for P38665 (Kluyveromyces lactis)
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60S ribosomal protein L25Z [auth XX]121Kluyveromyces lactisMutation(s): 0 
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Find proteins for P48045 (Kluyveromyces lactis)
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KLLA0B05742pAA [auth YY]125Kluyveromyces lactisMutation(s): 0 
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KLLA0E03455pBA [auth ZZ]134Kluyveromyces lactisMutation(s): 0 
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RPL28CA [auth aa]147Kluyveromyces lactisMutation(s): 0 
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KLLA0D16071pDA [auth bb]57Kluyveromyces lactisMutation(s): 0 
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60S ribosomal protein L30EA [auth cc]97Kluyveromyces lactisMutation(s): 0 
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Find proteins for P38664 (Kluyveromyces lactis)
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KLLA0B02937pFA [auth dd]106Kluyveromyces lactisMutation(s): 0 
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KLLA0E06843pGA [auth ee]122Kluyveromyces lactisMutation(s): 0 
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KLLA0D07405pHA [auth ff]105Kluyveromyces lactisMutation(s): 0 
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KLLA0C08371pIA [auth gg]121Kluyveromyces lactisMutation(s): 0 
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KLLA0F05247pJA [auth hh]116Kluyveromyces lactisMutation(s): 0 
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60S ribosomal protein L36KA [auth ii]98Kluyveromyces lactisMutation(s): 0 
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Ribosomal protein L37LA [auth jj]85Kluyveromyces lactisMutation(s): 0 
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KLLA0C18216pMA [auth kk]76Kluyveromyces lactisMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39NA [auth ll]49Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Ubiquitin fusion proteinOA [auth mm]51Kluyveromyces lactisMutation(s): 0 
Gene Names: ubi1
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Entity ID: 42
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60S ribosomal protein L41-APA [auth nn]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41A, RPL47A, YL41A, YDL184C, D1290
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60S ribosomal protein L44QA [auth oo]101Kluyveromyces lactisMutation(s): 0 
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Find proteins for P31027 (Kluyveromyces lactis)
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0E05941pRA [auth pp]87Kluyveromyces lactisMutation(s): 0 
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Ribosomal proteinSA [auth qq]217Kluyveromyces lactisMutation(s): 0 
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60S acidic ribosomal protein P0TA [auth rr]195Kluyveromyces lactisMutation(s): 0 
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uL11UA [auth KK]147Kluyveromyces lactisMutation(s): 0 
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Entity ID: 48
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40S ribosomal protein S0VA [auth A]206Kluyveromyces lactisMutation(s): 0 
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Entity ID: 49
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40S ribosomal protein S1WA [auth B]214Kluyveromyces lactisMutation(s): 0 
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Entity ID: 50
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KLLA0F09812pXA [auth C]217Kluyveromyces lactisMutation(s): 0 
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Entity ID: 51
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KLLA0D08305pYA [auth D]223Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S4ZA [auth E]260Kluyveromyces lactisMutation(s): 0 
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KLLA0D10659pAB [auth F]206Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S6BB [auth G]226Kluyveromyces lactisMutation(s): 0 
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Entity ID: 55
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KLLA0C13519pCB [auth H]184Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S8DB [auth I]200Kluyveromyces lactisMutation(s): 0 
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KLLA0E23673pEB [auth J]182Kluyveromyces lactisMutation(s): 0 
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Entity ID: 58
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KLLA0B08173pFB [auth K]96Kluyveromyces lactisMutation(s): 0 
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KLLA0A10483pGB [auth L]155Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S12HB [auth M]122Kluyveromyces lactisMutation(s): 0 
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KLLA0F18040pIB [auth N]150Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S14JB [auth O]127Kluyveromyces lactisMutation(s): 0 
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KLLA0F07843pKB [auth P]123Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S16LB [auth Q]141Kluyveromyces lactisMutation(s): 0 
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KLLA0B01474pMB [auth R]129Kluyveromyces lactisMutation(s): 0 
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KLLA0B01562pNB [auth S]145Kluyveromyces lactisMutation(s): 0 
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KLLA0A07194pOB [auth T]143Kluyveromyces lactisMutation(s): 0 
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KLLA0F25542pPB [auth U]106Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S21QB [auth V]87Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S22RB [auth W]129Kluyveromyces lactisMutation(s): 0 
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Entity ID: 71
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RPS23SB [auth X]145Kluyveromyces lactisMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S24TB [auth Y]134Kluyveromyces lactisMutation(s): 0 
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Entity ID: 73
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KLLA0B06182pUB [auth Z]70Kluyveromyces lactisMutation(s): 0 
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KLLA0D05115pVB [auth a]100Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S27WB [auth b]82Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S28XB [auth c]63Kluyveromyces lactisMutation(s): 0 
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40S ribosomal protein S29YB [auth d]53Kluyveromyces lactisMutation(s): 0 
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Entity ID: 78
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KLLA0C04809pZB [auth e]55Kluyveromyces lactisMutation(s): 0 
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Ubiquitin-40S ribosomal protein S27aAC [auth f]69Kluyveromyces lactisMutation(s): 0 
UniProt
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KLLA0E12277pBC [auth g]324Kluyveromyces lactisMutation(s): 0 
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Eft2pEC [auth 1]827Saccharomyces cerevisiae P283Mutation(s): 0 
Gene Names: Eft2, P283_D20866
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25S ribosomal RNAA [auth 5]3,270Kluyveromyces lactis
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5S ribosomal RNAB [auth 7]121Kluyveromyces lactis
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5.8S ribosomal RNAC [auth 8]157Kluyveromyces lactis
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18S ribosomal RNACC [auth 2]1,798Kluyveromyces lactis
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cricket paralysis virus IRESDC [auth 4]190Cricket paralysis virus
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP
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NF [auth 1]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N		 Ligand Interaction
6EM
Query on 6EM
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OF [auth 1](2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium
C7 H17 N2 O
LPOFDMFKBRMZLU-LURJTMIESA-O		 Ligand Interaction
ZN
Query on ZN
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HC [auth jj],
IC [auth mm],
JC [auth oo],
LC [auth a],
MC [auth b],
HC [auth jj],
IC [auth mm],
JC [auth oo],
LC [auth a],
MC [auth b],
NC [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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AD [auth 2],
AE [auth 2],
AF [auth 2],
BD [auth 2],
BE [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
FC [auth 5],
FD [auth 2],
FE [auth 2],
FF [auth 2],
GC [auth 5],
GD [auth 2],
GE [auth 2],
GF [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth 2],
KC [auth N],
KD [auth 2],
KE [auth 2],
KF [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth 2],
MD [auth 2],
ME [auth 2],
MF [auth 1],
ND [auth 2],
NE [auth 2],
OC [auth f],
OD [auth 2],
OE [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8

Structure Validation

View Full Validation Report



View more in-depth experimental data
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: 2018-03-28
    Changes: Advisory
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations