ISDA: 4V6Z

Deposition Date 2013-10-14

Release Date 2014-07-09

Last Version Date 2024-10-30

Entry Detail

PDB ID:

4V6Z

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 83333)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

12.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download 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
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.

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

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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Disease

Primary Citation of related structures