3JAP

Structure of a partial yeast 48S preinitiation complex in closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6GSN


Literature

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.

Llacer, J.L.Hussain, T.Marler, L.Aitken, C.E.Thakur, A.Lorsch, J.R.Hinnebusch, A.G.Ramakrishnan, V.

(2015) Mol Cell 59: 399-412

  • DOI: https://doi.org/10.1016/j.molcel.2015.06.033
  • Primary Citation of Related Structures:  
    3JAM, 3JAP

  • PubMed Abstract: 

    Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uS2D [auth A]254Kluyveromyces lactisMutation(s): 0 
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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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS1E [auth B]255Kluyveromyces lactisMutation(s): 0 
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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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uS5F [auth C]259Kluyveromyces lactisMutation(s): 0 
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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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uS3G [auth D]237Kluyveromyces 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: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS4H [auth E]261Kluyveromyces lactisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uS7I [auth F]227Kluyveromyces lactisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eS6J [auth G]236Kluyveromyces lactisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
eS7K [auth H]190Kluyveromyces lactisMutation(s): 0 
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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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eS8L [auth I]201Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CMG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uS4M [auth J]188Kluyveromyces lactisMutation(s): 0 
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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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS10N [auth K]106Kluyveromyces 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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uS17O [auth L]156Kluyveromyces lactisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eS12P [auth M]134Kluyveromyces lactisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uS15Q [auth N]151Kluyveromyces lactisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uS11R [auth O]137Kluyveromyces 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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uS19S [auth P]142Kluyveromyces 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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS9T [auth Q]143Kluyveromyces 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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
eS17U [auth R]136Kluyveromyces 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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS13V [auth S]146Kluyveromyces 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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eS19W [auth T]144Kluyveromyces 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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS10X [auth U]117Kluyveromyces 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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eS21Y [auth V]87Kluyveromyces 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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uS8Z [auth W]130Kluyveromyces lactisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS12AA [auth X]145Kluyveromyces lactisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS24BA [auth Y]135Kluyveromyces lactisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eS25CA [auth Z]108Kluyveromyces lactisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS26DA [auth a]119Kluyveromyces lactisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eS27EA [auth b]82Kluyveromyces lactisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS28FA [auth c]67Kluyveromyces lactisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
uS14GA [auth d]56Kluyveromyces lactisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eS30HA [auth e]63Kluyveromyces lactisMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eS31IA [auth f]150Kluyveromyces lactisMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1JA [auth g]326Kluyveromyces lactisMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL41KA [auth h]25Kluyveromyces lactisMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eIF1ALA [auth i]153Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eIF2 alphaMA [auth j]304Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eIF2 gammaNA [auth k]527Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eIF2 betaOA [auth l]285Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eIF1PA [auth m]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3aQA [auth o]588Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3cRA [auth p]652Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32497 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32497
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3iSA [auth q]347Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40217
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3bTA [auth r]31Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP06103
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3gUA [auth s]52Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A6ZZ25 (Saccharomyces cerevisiae (strain YJM789))
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UniProt GroupA6ZZ25
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Entity ID: 1
MoleculeChains LengthOrganismImage
Met-tRNAi (U31:A39 variant)A [auth 1]75Kluyveromyces lactis
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S rRNAB [auth 2]1,781Kluyveromyces lactis
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNAC [auth 3]25synthetic construct
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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CE [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MET
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AE [auth k]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN
Query on ZN

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DE [auth l],
XD [auth a],
YD [auth b],
ZD [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 2]
AC [auth 2]
AD [auth 2]
BB [auth 2]
BC [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth k],
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],
JB [auth 2],
JC [auth 2],
JD [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection, Other
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description