3JCJ

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.

Sprink, T.Ramrath, D.J.Yamamoto, H.Yamamoto, K.Loerke, J.Ismer, J.Hildebrand, P.W.Scheerer, P.Burger, J.Mielke, T.Spahn, C.M.

(2016) Sci Adv 2: e1501502-e1501502

  • DOI: https://doi.org/10.1126/sciadv.1501502
  • Primary Citation of Related Structures:  
    3JCJ, 3JCN

  • PubMed Abstract: 

    Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.


  • Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18B [auth 1]75Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21C [auth 2]71Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20D [auth 3]87Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2G [auth B]273Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3H [auth C]209Escherichia coliMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L4I [auth D]201Escherichia coliMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L5J [auth E]179Escherichia coliMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L6K [auth F]177Escherichia coliMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L9L [auth G]149Escherichia coliMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L11M [auth H]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L13N [auth I]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14O [auth J]123Escherichia coliMutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L15P [auth K]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16Q [auth L]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17R [auth M]127Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L18S [auth N]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19T [auth O]115Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth P]118Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth Q]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22W [auth R]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23X [auth S]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24Y [auth T]104Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L25Z [auth U]94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27AA [auth V]85Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L28BA [auth W]78Escherichia coliMutation(s): 0 
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Entity ID: 29
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50S ribosomal protein L29CA [auth X]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30DA [auth Y]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32EA [auth Z]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33FA [auth a]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34GA [auth b]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35HA [auth c]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36IA [auth d]38Escherichia coliMutation(s): 0 
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50S ribosomal protein L10JA [auth e]165Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2KA [auth f]890Escherichia coliMutation(s): 0 
Gene Names: infBgicDssyGb3168JW3137
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Entity ID: 39
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30S ribosomal protein S3MA [auth h]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S2NA [auth j]241Escherichia coliMutation(s): 0 
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30S ribosomal protein S5OA [auth k]167Escherichia coliMutation(s): 0 
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30S ribosomal protein S4PA [auth l]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S7QA [auth m]179Escherichia coliMutation(s): 0 
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30S ribosomal protein S6RA [auth n]135Escherichia coliMutation(s): 0 
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30S ribosomal protein S9SA [auth o]130Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8TA [auth p]130Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11UA [auth q]129Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10VA [auth r]102Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13WA [auth s]118Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12XA [auth t]124Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15YA [auth u]89Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
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UniProt GroupP0ADZ4
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14AB [auth w]101Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12))
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UniProt GroupP0AG59
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17BB [auth x]84Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16CB [auth y]82Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19DB [auth z]92Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
5S ribosomal RNAA [auth 0]118Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
messenger RNAE [auth 4]52Escherichia coli
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Entity ID: 6
MoleculeChains LengthOrganismImage
23S ribosomal RNAF [auth A]2,904Escherichia coli
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Entity ID: 38
MoleculeChains LengthOrganismImage
16S ribosomal RNALA [auth g]1,542Escherichia coli
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Entity ID: 52
MoleculeChains LengthOrganismImage
tRNAZA [auth v]77Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

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PG [auth f]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FME
Query on FME

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SI [auth v]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN

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OG [auth d]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AG [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth g],
AI [auth g],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth g],
BI [auth g],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth g],
CI [auth g],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth g],
DI [auth g],
EB [auth 3],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth g],
EI [auth g],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth g],
FI [auth g],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth g],
GI [auth g],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth g],
HI [auth g],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth g],
II [auth g],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth g],
JI [auth g],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth g],
KI [auth g],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth g],
LI [auth g],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth B],
MH [auth g],
MI [auth g],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth d],
NH [auth g],
NI [auth g],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OH [auth g],
OI [auth g],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PH [auth g],
PI [auth g],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth g],
QH [auth g],
QI [auth g],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth g],
RH [auth g],
RI [auth g],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth g],
SH [auth g],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth g],
TH [auth g],
TI [auth w],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth g],
UH [auth g],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth g],
VH [auth g],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth g],
WH [auth g],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth g],
XH [auth g],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth g],
YH [auth g],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth g],
ZH [auth g]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection