4V78 image
Deposition Date 2013-10-14
Release Date 2014-07-09
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4V78
Keywords:
RIBOSOME
Title:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 83333)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
20.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V78 validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:fMet-Val-tRNA-Val
Chain IDs:V (auth: A1)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:tRNA-fMet
Chain IDs:X (auth: A3)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:U (auth: AA)
Chain Length:1533
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:A (auth: AB)
Chain Length:220
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:B (auth: AC)
Chain Length:208
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:C (auth: AD)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:D (auth: AE)
Chain Length:152
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:E (auth: AF)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02358 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:F (auth: AG)
Chain Length:152
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:G (auth: AH)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7W7 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:H (auth: AI)
Chain Length:128
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7X3 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:I (auth: AJ)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:J (auth: AK)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:K (auth: AL)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: AM)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:M (auth: AN)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:N (auth: AO)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: AP)
Chain Length:81
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:P (auth: AQ)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: AR)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: AS)
Chain Length:81
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: AT)
Chain Length:86
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:T (auth: AU)
Chain Length:53
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:WA (auth: B0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:XA (auth: B1)
Chain Length:52
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:YA (auth: B2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:ZA (auth: B3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:AB (auth: B4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:DB (auth: B5)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L0 Pfam ID:PF00687
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:BB (auth: BA)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:CB (auth: BB)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:Y (auth: BC)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Z (auth: BD)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:AA (auth: BE)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:BA (auth: BF)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:CA (auth: BG)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:DA (auth: BH)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:EA (auth: BI)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:FA (auth: BJ)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:GA (auth: BK)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:HA (auth: BL)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:IA (auth: BM)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:JA (auth: BN)
Chain Length:121
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:KA (auth: BO)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:LA (auth: BP)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:MA (auth: BQ)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:NA (auth: BR)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:OA (auth: BS)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:PA (auth: BT)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:QA (auth: BU)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:RA (auth: BV)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:SA (auth: BW)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:TA (auth: BX)
Chain Length:79
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:UA (auth: BY)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7M6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:VA (auth: BZ)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU V U 4-THIOURIDINE-5'-MONOPHOSPHATE
5MU V U 5-METHYLURIDINE 5'-MONOPHOSPHATE
6MZ V A N6-METHYLADENOSINE-5'-MONOPHOSPHATE
7MG V G ?
H2U X U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
OMC X C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
PSU V U PSEUDOURIDINE-5'-MONOPHOSPHATE
Ligand Molecules
FME
VAL
Primary Citation
Energy barriers and driving forces in tRNA translocation through the ribosome.
Nat.Struct.Mol.Biol. 20 1390 1396 (2013)
PMID: 24186064 DOI: 10.1038/nsmb.2690

Abstact

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.

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Primary Citation of related structures
4V78
3J5F
3J5G
3J4V
3J52
3J4W
3J4X
3J4Z
3J50
3J4Y
3J51
3J53
3J54
3J55
3J56
3J57
3J58
3J59
3J5A
3J5B
3J5C
3J5D
3J5E
3J5H
3J5I
3J5J
3J5K