4V74

70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17 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

Energy barriers and driving forces in tRNA translocation through the ribosome.

Bock, L.V.Blau, C.Schroder, G.F.Davydov, I.I.Fischer, N.Stark, H.Rodnina, M.V.Vaiana, A.C.Grubmuller, H.

(2013) Nat.Struct.Mol.Biol. 20: 1390-1396

  • DOI: 10.1038/nsmb.2690
  • Primary Citation of Related Structures:  3J4V, 3J4W, 3J4X, 3J4Y, 3J4Z, 3J50, 3J51, 3J52, 3J53, 3J54, 3J55, 3J56, 3J57, 3J58, 3J59, 3J5A, 3J5B, 3J5D, 3J5C, 3J5E, 3J5F, 3J5G, 3J5H, 3J5I, 3J5J, 3J5K, 4V6Y, 4V6Z, 4V70, 4V71, 4V72, 4V73, 4V75, 4V76, 4V77, 4V78, 4V79, 4V7A

  • PubMed Abstract: 
  • During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state mod ...

    During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.


    Organizational Affiliation

    1] Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
220Escherichia coli (strain K12)Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
208Escherichia coli (strain K12)Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
206Escherichia coli (strain K12)Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
152Escherichia coli (strain K12)Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
101Escherichia coli (strain K12)Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
152Escherichia coli (strain K12)Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
130Escherichia coli (strain K12)Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
128Escherichia coli (strain K12)Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
100Escherichia coli (strain K12)Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
118Escherichia coli (strain K12)Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
124Escherichia coli (strain K12)Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
115Escherichia coli (strain K12)Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN
101Escherichia coli (strain K12)Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Escherichia coli (strain K12)Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
81Escherichia coli (strain K12)Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
82Escherichia coli (strain K12)Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
57Escherichia coli (strain K12)Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
81Escherichia coli (strain K12)Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
86Escherichia coli (strain K12)Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
53Escherichia coli (strain K12)Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BC
273Escherichia coli (strain K12)Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BD
209Escherichia coli (strain K12)Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BE
201Escherichia coli (strain K12)Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BF
179Escherichia coli (strain K12)Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BG
177Escherichia coli (strain K12)Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BH
149Escherichia coli (strain K12)Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BI
142Escherichia coli (strain K12)Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BJ
142Escherichia coli (strain K12)Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BK
123Escherichia coli (strain K12)Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BL
144Escherichia coli (strain K12)Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BM
136Escherichia coli (strain K12)Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BN
121Escherichia coli (strain K12)Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BO
117Escherichia coli (strain K12)Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BP
115Escherichia coli (strain K12)Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BQ
118Escherichia coli (strain K12)Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BR
103Escherichia coli (strain K12)Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BS
110Escherichia coli (strain K12)Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BT
94Escherichia coli (strain K12)Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BU
104Escherichia coli (strain K12)Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BV
94Escherichia coli (strain K12)Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BW
80Escherichia coli (strain K12)Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
BX
79Escherichia coli (strain K12)Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY
63Escherichia coli (strain K12)Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ
59Escherichia coli (strain K12)Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B0
57Escherichia coli (strain K12)Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B1
52Escherichia coli (strain K12)Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B2
46Escherichia coli (strain K12)Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B3
65Escherichia coli (strain K12)Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B4
38Escherichia coli (strain K12)Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
B5
234Escherichia coli (strain K12)Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 21
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1533Escherichia coli K-12
Entity ID: 22
MoleculeChainsLengthOrganism
fMet-Val-tRNA-ValA176Escherichia coli K-12
Entity ID: 23
MoleculeChainsLengthOrganism
5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'A215N/A
Entity ID: 24
MoleculeChainsLengthOrganism
tRNA-fMetA377Escherichia coli K-12
Entity ID: 54
MoleculeChainsLengthOrganism
23S ribosomal RNABA2903Escherichia coli K-12
Entity ID: 55
MoleculeChainsLengthOrganism
5S ribosomal RNABB118Escherichia coli K-12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download SDF File 
Download CCD File 
BA
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
VAL
Query on VAL

Download SDF File 
Download CCD File 
A1
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  10 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A1, A3
RNA LINKINGC9 H13 N2 O9 PU
CM0
Query on CM0
A1
RNA LINKINGC11 H15 N2 O12 P

--

NH2
Query on NH2
AB, AC, AE, AF, AG, AJ, AM, AP, AQ, AR, AS, AU, B1, BC, BK, BN, BT, BU
NON-POLYMERH2 N

--

6MZ
Query on 6MZ
A1
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
A3
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
A1, A3
RNA LINKINGC9 H13 N2 O8 P SU
7MG
Query on 7MG
A1
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
A1, A3
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
A3
RNA LINKINGC9 H15 N2 O9 PU
ACE
Query on ACE
AB, AE, AG, AI, AJ, AK, AQ, AR, AS, AT, AU, B1, BW, BX
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other
  • Version 1.2: 2015-04-08
    Type: Other