4V6N

Structural characterization of mRNA-tRNA translocation intermediates (50S ribosome of class2 of the six classes)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 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.USA 109: 6094-6099

  • DOI: 10.1073/pnas.1201288109
  • Primary Citation of Related Structures:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
AC
234Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AD
272Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AE
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AF
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AG
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AH
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
AI
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
AJ
164Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplJ
Find proteins for P0A7J3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AK
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AL
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AM
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AN
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AO
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AP
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AQ
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AR
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AS
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AT
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AU
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AV
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AW
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AX
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
AY
84Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
AZ
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
A0
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
A1
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
A2
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmE
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M9
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
A3
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A4
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A5
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A6
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A7
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
BE
240Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BF
232Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
BG
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
BH
166Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
BI
135Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
BJ
178Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
BK
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
BL
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
BM
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
BN
128Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BO
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
BP
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
BQ
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BR
88Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q8X9M2 (Escherichia coli O157:H7)
Go to UniProtKB:  Q8X9M2
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
BS
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
BT
83Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
BU
74Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BV
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BW
86Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
BX
70Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 1
MoleculeChainsLengthOrganism
5S ribosomal RNAAA120Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S ribosomal RNAAB2904Escherichia coli
Entity ID: 35
MoleculeChainsLengthOrganism
16S ribosomal RNABA1542Escherichia coli
Entity ID: 36
MoleculeChainsLengthOrganism
A site tRNABB76Escherichia coli
Entity ID: 37
MoleculeChainsLengthOrganism
mRNABC47Escherichia coli
Entity ID: 38
MoleculeChainsLengthOrganism
P site tRNABD77Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

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

Download SDF File 
Download CCD File 
BB
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Modified Residues  19 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
AB, BA, BB, BD
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
AB, BA
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
AB
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
AB
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
AB
RNA LINKINGC11 H16 N5 O8 PG
OMC
Query on OMC
AB, BB, BD
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
BA
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
BB, BD
RNA LINKINGC9 H13 N2 O8 P SU
CH
Query on CH
AB
RNA LINKINGC9 H15 N3 O8 PC
MIA
Query on MIA
BB
RNA LINKINGC16 H26 N5 O7 P SA
2MG
Query on 2MG
AB, BA
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
BA
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
AB
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
AB, BA, BB
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
AB, BB, BD
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
AB
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
BA
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
AB
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
AB, BB, BD
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.1 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: 2015-04-01
    Type: Other
  • Version 2.0: 2018-07-18
    Type: Data collection, Database references, Polymer sequence