Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 50-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwx Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 50-mer -A2BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvw 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2195471.25 
• Atom Count: 147653 
• Residue Count: 10730 
• Unique protein chains: 50
• Unique nucleic acid chains: 6

4V6Z

E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b)

• DOI: 10.2210/pdb4V6Z/pdb
• Entry 4V6Z supersedes 3J4W, 3J4X
• EMDataResource: EMD-2472

• Classification: RIBOSOME
• Organism(s): Escherichia coli (strain K12), Escherichia coli K-12


• Deposited: 2013-10-14 Released: 2014-07-09 
• Deposition Author(s): Blau, C., Bock, L.V., Schroder, G.F., Davydov, I., Fischer, N., Stark, H., Rodnina, M.V., Vaiana, A.C., Grubmuller, H.

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 24186064 
• DOI: 10.1038/nsmb.2690
• Primary Citation of Related Structures:  
  4V7A, 4V79, 4V78, 4V77, 4V76, 4V75, 4V74, 4V73, 4V72, 4V71, 4V70, 4V6Y, 3J5K, 3J5J, 3J5I, 3J5H, 3J5G, 3J5F, 3J5E, 3J5C, 3J5D, 3J5B, 3J5A, 3J59, 3J58, 3J57, 3J56, 3J55, 3J54, 3J53, 3J52, 3J51, 3J50, 3J4Z, 3J4Y, 3J4X, 3J4W, 3J4V


• 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 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
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S2	AB	220	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S3	AC	208	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S4	AD	206	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7V8

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S5	AE	152	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7W1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S6	AF	101	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12)) Go to UniProtKB:  P02358

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S7	AG	152	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12)) Go to UniProtKB:  P02359

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S8	AH	130	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7W7

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S9	AI	128	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7X3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S10	AJ	100	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R5

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S11	AK	118	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R9

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S12	AL	124	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7S3

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S13	AM	115	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7S9

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S14	AN	101	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG59

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S15	AO	89	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsO (secC)
Find proteins for P0ADZ4 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADZ4

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S16	AP	81	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T3

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S17	AQ	82	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG63

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S18	AR	57	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7T7

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S19	AS	81	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U3

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S20	AT	86	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7U7

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
30S ribosomal protein S21	AU	53	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12)) Go to UniProtKB:  P68679

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L2	BC	273	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12)) Go to UniProtKB:  P60422

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L3	BD	209	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12)) Go to UniProtKB:  P60438

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L4	BE	201	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12)) Go to UniProtKB:  P60723

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L5	BF	179	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12)) Go to UniProtKB:  P62399

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L6	BG	177	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG55

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L9	BH	149	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7R1

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L11	BI	142	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7J7

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L13	BJ	142	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AA10

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L14	BK	123	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY3

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L15	BL	144	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12)) Go to UniProtKB:  P02413

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L16	BM	136	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADY7

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L17	BN	121	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG44

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L18	BO	117	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12)) Go to UniProtKB:  P0C018

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L19	BP	115	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7K6

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L20	BQ	118	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L3

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L21	BR	103	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG48

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L22	BS	110	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12)) Go to UniProtKB:  P61175

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L23	BT	94	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0ADZ0

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L24	BU	104	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12)) Go to UniProtKB:  P60624

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L25	BV	94	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12)) Go to UniProtKB:  P68919

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L27	BW	80	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L8

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L28	BX	79	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M2

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L29	BY	63	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7M6

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L30	BZ	59	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12)) Go to UniProtKB:  P0AG51

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L32	B0	57	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N4

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L33	B1	52	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7N9

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L34	B2	46	Escherichia 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: 52
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L35	B3	65	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q1

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L36	B4	38	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Q6

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details
50S ribosomal protein L1	B5	234	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: rplA
Find proteins for P0A7L0 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7L0

Entity ID: 21
Molecule	Chains	Length	Organism
16S ribosomal RNA	AA	1533	Escherichia coli K-12

Entity ID: 22
Molecule	Chains	Length	Organism
fMet-Val-tRNA-Val	A1	76	Escherichia coli K-12

Entity ID: 23
Molecule	Chains	Length	Organism
5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'	A2	15	N/A

Entity ID: 24
Molecule	Chains	Length	Organism
tRNA-fMet	A3	77	Escherichia coli K-12

Entity ID: 54
Molecule	Chains	Length	Organism
23S ribosomal RNA	BA	2903	Escherichia coli K-12

Entity ID: 55
Molecule	Chains	Length	Organism
5S ribosomal RNA	BB	118	Escherichia coli K-12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FME	BA	N-FORMYLMETHIONINE C6 H11 N O3 S PYUSHNKNPOHWEZ-YFKPBYRVSA-N
VAL	A1	VALINE C5 H11 N O2 KZSNJWFQEVHDMF-BYPYZUCNSA-N

Modified Residues  10 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PSU	A1, A3	RNA LINKING	C9 H13 N2 O9 P		U
CM0	A1	RNA LINKING	C11 H15 N2 O12 P		--
NH2	AB, AC, AE, AF, AG, AJ, AM, AP, AQ, AR, AS, AU, B1, BC, BK, BN, BT, BU	NON-POLYMER	H2 N		--
6MZ	A1	RNA LINKING	C11 H16 N5 O7 P		A
OMC	A3	RNA LINKING	C10 H16 N3 O8 P		C
4SU	A1, A3	RNA LINKING	C9 H13 N2 O8 P S		U
7MG	A1	RNA LINKING	C11 H18 N5 O8 P		G
5MU	A1, A3	RNA LINKING	C10 H15 N2 O9 P		U
H2U	A3	RNA LINKING	C9 H15 N2 O9 P		U
ACE	AB, AE, AG, AI, AJ, AK, AQ, AR, AS, AT, AU, B1, BW, BX	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 12 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-14 
• Released Date: 2014-07-09 
• Deposition Author(s): Blau, C., Bock, L.V., Schroder, G.F., Davydov, I., Fischer, N., Stark, H., Rodnina, M.V., Vaiana, A.C., Grubmuller, H.
• This entry supersedes: 3J4W 3J4X

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
• Version 2.0: 2018-07-18
  Type: Data collection, Polymer sequence
• Version 2.1: 2018-09-05
  Type: Data collection, Experimental preparation, Refinement description
• Version 2.2: 2019-12-18
  Type: Database references, Derived calculations, Other