ISDA: 4V9J

Deposition Date 2013-04-23

Release Date 2014-07-09

Last Version Date 2023-12-06

Entry Detail

PDB ID:

4V9J

Keywords:

RIBOSOME/ANTIBIOTIC

Title:

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 262724)
Escherichia coli (Taxon ID: 562)
Streptomyces (Taxon ID: 1883)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.86 Å

R-Value Free:

0.31

R-Value Work:

0.26

R-Value Observed:

0.26

Space Group:

C 1 2 1

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:T (auth: AA), CC (auth: CA)
Chain Length:1511
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:A (auth: AB), JB (auth: CB)
Chain Length:235
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62662 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), KB (auth: CC)
Chain Length:207
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62663 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), LB (auth: CD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62664 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), MB (auth: CE)
Chain Length:151
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62665 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), NB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62666 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), OB (auth: CG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62667 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), PB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62668 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), QB (auth: CI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62669 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), RB (auth: CJ)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62653 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), SB (auth: CK)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62654 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), TB (auth: CL)
Chain Length:125
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P61941 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), UB (auth: CM)
Chain Length:125
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62655 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:M (auth: AN), VB (auth: CN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62656 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), WB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62657 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), XB (auth: CP)
Chain Length:84
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62238 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), YB (auth: CQ)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62658 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), ZB (auth: CR)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62659 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), AC (auth: CS)
Chain Length:79
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62660 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), BC (auth: CT)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62661 Pfam ID:PF01649

Polymer Type:polypeptide(L)
Molecule:Viomycin
Chain IDs:X (auth: AU), GC (auth: CU)
Chain Length:6
Number of Molecules:2
Biological Source:Streptomyces

Polymer Type:polyribonucleotide
Molecule:messenger RNA
Chain IDs:U (auth: AV), DC (auth: CV)
Chain Length:18
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:tRNA-Met
Chain IDs:V (auth: AW), EC (auth: CW)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Chain IDs:W (auth: AY), FC (auth: CY)
Chain Length:687
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN5 Pfam ID:PF14492, PF00009, PF03144, PF03764, PF00679

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:SA (auth: B0), BD (auth: D0)
Chain Length:84
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR3 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: B1), CD (auth: D1)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72G84 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: B2), FD (auth: D2)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I12 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: B3), GD (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I22 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:UA (auth: B4), DD (auth: D4)
Chain Length:35
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JR0 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: B5), HD (auth: D5)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62652 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: B6), ID (auth: D6)
Chain Length:50
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GW3 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: B7), JD (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: B8), KD (auth: D8)
Chain Length:64
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L77 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:CB (auth: B9), LD (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I28 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:IB (auth: BA), RD (auth: DA)
Chain Length:2879
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:HB (auth: BB), QD (auth: DB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:Y (auth: BC), HC (auth: DC)
Chain Length:228
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GV9 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:Z (auth: BD), IC (auth: DD)
Chain Length:275
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I07 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:AA (auth: BE), JC (auth: DE)
Chain Length:103
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I04 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:BA (auth: BF), KC (auth: DF)
Chain Length:31
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I05 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:CA (auth: BG), LC (auth: DG)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ0 Pfam ID:PF00673, PF00281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:DA (auth: BH), MC (auth: DH)
Chain Length:167
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I19 Pfam ID:PF00347

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Chain IDs:EA (auth: BJ), NC (auth: DJ)
Chain Length:170
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:FA (auth: BK), OC (auth: DK)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62442 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:VA (auth: BN), ED (auth: DN)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IN1 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: BO), PC (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I14 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: BP), QC (auth: DP)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I23 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: BQ), RC (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I11 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: BR), SC (auth: DR)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I33 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: BS), TC (auth: DS)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I20 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: BT), UC (auth: DT)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JU9 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: BU), VC (auth: DU)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L76 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: BV), WC (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR2 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: BW), XC (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I09 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: BX), YC (auth: DX)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I06 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: BY), ZC (auth: DY)
Chain Length:107
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I15 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: BZ), AD (auth: DZ)
Chain Length:185
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7/L12
Gene (Uniprot):rplL
Chain IDs:DB (auth: Be), MD (auth: De)
Chain Length:103
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GS2 Pfam ID:PF00542

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7/L12
Chain IDs:EB (auth: Bf), FB (auth: Bg), ND (auth: Df), OD (auth: Dg)
Chain Length:31
Number of Molecules:4
Biological Source:Thermus thermophilus

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7/L12
Chain IDs:GB (auth: Bh), PD (auth: Dh)
Chain Length:167
Number of Molecules:2
Biological Source:Thermus thermophilus

Ligand Molecules

GNP

Peptide-like Molecules

PRD_000226

Primary Citation

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Zhou, J, Lancaster, L, Donohue, J.P, Noller, H.F.Show

Science 340 1236086 1236086 (2013)

PMID: 23812722 DOI: 10.1126/science.1236086

Abstact

Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.

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Protein

Chemical

Disease

Primary Citation of related structures