4V6Q

Structural characterization of mRNA-tRNA translocation intermediates (class 5 of the six classes)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structural characterization of mRNA-tRNA translocation intermediates.

Agirrezabala, X.Liao, H.Y.Schreiner, E.Fu, J.Ortiz-Meoz, R.F.Schulten, K.Green, R.Frank, J.

(2012) Proc Natl Acad Sci U S A 109: 6094-6099

  • DOI: 10.1073/pnas.1201288109
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersub ...

    Cryo-EM analysis of a wild-type Escherichia coli pretranslocational sample has revealed the presence of previously unseen intermediate substates of the bacterial ribosome during the first phase of translocation, characterized by intermediate intersubunit rotations, L1 stalk positions, and tRNA configurations. Furthermore, we describe the domain rearrangements in quantitative terms, which has allowed us to characterize the processivity and coordination of the conformational reorganization of the ribosome, along with the associated changes in tRNA ribosome-binding configuration. The results are consistent with the view of the ribosome as a molecular machine employing Brownian motion to reach a functionally productive state via a series of substates with incremental changes in conformation.


    Organizational Affiliation

    Structural Biology Unit, CIC-bioGUNE, Bizkaia Technology Park, Derio 48160, Basque Country, Spain.



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AE
240Escherichia coliMutation(s): 0 
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AI
135Escherichia coliMutation(s): 0 
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AJ
178Escherichia coliMutation(s): 0 
Find proteins for P02359 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AL
129Escherichia coliMutation(s): 0 
Find proteins for P0A7X3 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AM
103Escherichia coliMutation(s): 0 
Find proteins for P0A7R5 (Escherichia coli (strain K12))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AN
128Escherichia coliMutation(s): 0 
Find proteins for P0A7R9 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AO
123Escherichia coliMutation(s): 0 
Find proteins for P0A7S3 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AP
117Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AQ
100Escherichia coliMutation(s): 0 
Find proteins for P0AG59 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AR
88Escherichia coliMutation(s): 0 
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AS
82Escherichia coliMutation(s): 0 
Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AT
83Escherichia coliMutation(s): 0 
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AU
74Escherichia coliMutation(s): 0 
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AV
91Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AW
86Escherichia coliMutation(s): 0 
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
BC
234Sulfolobus acidocaldariusMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
178Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
176Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BJ
164Sulfolobus acidocaldariusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK
141Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BL
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BM
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BN
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BO
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BQ
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BR
114Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BS
117Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BT
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BU
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BV
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BX
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BY
84Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BZ
77Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B0
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B1
58Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B2
70Escherichia coliMutation(s): 0 
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B3
56Escherichia coliMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B4
54Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B5
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B6
64Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AK
129Escherichia coliMutation(s): 0 
Find proteins for P0A7W7 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AX
70Escherichia coliMutation(s): 0 
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
272Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BP
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BW
103Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B7
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AF
232Escherichia coliMutation(s): 0 
Find proteins for P0A7V3 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AG
205Escherichia coliMutation(s): 0 
Find proteins for P0A7V8 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AH
166Escherichia coliMutation(s): 0 
Find proteins for P0A7W1 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1542Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
A site tRNAAB76Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
mRNAAC47Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
5S ribomosomal RNABA120Escherichia coli

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Entity ID: 26
MoleculeChainsLengthOrganism
23S ribomosomal RNABB2904Escherichia coli

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Entity ID: 4
MoleculeChainsLengthOrganism
P site tRNAAD77Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download CCD File 
AB
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
FME
Query on FME

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-01
    Changes: Other
  • Version 2.0: 2018-07-18
    Changes: Data collection, Database references, Polymer sequence
  • Version 3.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2019-12-18
    Changes: Other