3JCN

Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association: Initiation Complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 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: 10.1126/sciadv.1501502
  • Structures With Same Primary Citation

  • 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 ...

    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: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
I
142Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
115Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
118Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
R
103Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
110Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
104Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
94Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
85Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
78Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
46Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
63Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
59Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-2
b
890Escherichia coliMutation(s): 0 
Gene Names: infBgicDssyGb3168JW3137
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
233Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
d
241Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
f
159Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
g
206Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
h
179Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
i
135Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
65Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
j
130Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
k
130Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
l
129Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
m
102Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
n
118Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
o
124Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
p
89Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
q
101Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
r
84Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
s
82Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
38Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
t
92Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
u
75Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
w
71Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
x
87Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsLengthOrganism
16S ribosomal RNAa1542Escherichia coli

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Entity ID: 52
MoleculeChainsLengthOrganism
tRNAv77Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganism
messenger RNAz6Escherichia coli

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Entity ID: 6
MoleculeChainsLengthOrganism
23S ribosomal RNAA2904Escherichia coli

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Entity ID: 7
MoleculeChainsLengthOrganism
5S ribosomal RNAB120Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
b
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
FME
Query on FME

Download CCD File 
v
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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