ISDA: 4V5F

Deposition Date 2009-09-01

Release Date 2014-07-09

Last Version Date 2024-10-16

Entry Detail

PDB ID:

4V5F

Keywords:

RIBOSOME

Title:

The structure of the ribosome with elongation factor G trapped in the post-translocational state

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)
THERMUS THERMOPHILUS (Taxon ID: 300852)
ESCHERICHIA COLI (Taxon ID: 83333)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.60 Å

R-Value Free:

0.26

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), KB (auth: CA)
Chain Length:1522
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:B (auth: AB), LB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80371 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), MB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80372 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:D (auth: AD), NB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80373 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:E (auth: AE), OB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ5 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:F (auth: AF), PB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP8 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), QB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), RB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), SB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80374 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), TB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN7 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), UB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80376 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), VB (auth: CL)
Chain Length:132
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), WB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14 TYPE Z
Chain IDs:N (auth: AN), XB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), YB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJ76 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), ZB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), AC (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), BC (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), CC (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP2 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), DC (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80380 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), EC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:E-SITE TRNA FMET OR P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)
Chain IDs:V (auth: AV), W (auth: AW), FC (auth: CV), GC (auth: CW)
Chain Length:77
Number of Molecules:4
Biological Source:ESCHERICHIA COLI

Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:X (auth: AX), HC (auth: CX)
Chain Length:25
Number of Molecules:2
Biological Source:synthetic construct

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:ELONGATION FACTOR G
Gene (Uniprot):fusA
Chain IDs:Y (auth: AY), IC (auth: CY)
Chain Length:691
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

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

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:Z (auth: B0), JC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60493 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L28
Gene (Uniprot):rpmB
Chain IDs:AA (auth: B1), KC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60494 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpmC
Chain IDs:BA (auth: B2), LC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpmD
Chain IDs:CA (auth: B3), MC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L31
Gene (Uniprot):rpmE
Chain IDs:DA (auth: B4), NC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJE1 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L32
Gene (Uniprot):rpmF
Chain IDs:EA (auth: B5), OC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80339 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L33
Gene (Uniprot):rpmG
Chain IDs:FA (auth: B6), PC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P35871 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L34
Gene (Uniprot):rpmH
Chain IDs:GA (auth: B7), QC (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:HA (auth: B8), RC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SKU1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L36
Gene (Uniprot):rpmJ
Chain IDs:IA (auth: B9), SC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:JA (auth: BA), TC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:KA (auth: BB), UC (auth: DB)
Chain Length:122
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:LA (auth: BC), VC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP7 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:MA (auth: BD), WC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60405 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:NA (auth: BE), XC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN8 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L4
Gene (Uniprot):rplD
Chain IDs:OA (auth: BF), YC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN9 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L5
Gene (Uniprot):rplE
Chain IDs:PA (auth: BG), ZC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:QA (auth: BH), AD (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L10
Chain IDs:RA (auth: BJ), BD (auth: DJ)
Chain Length:173
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:SA (auth: BK), CD (auth: DK)
Chain Length:147
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP6 Pfam ID:PF03946, PF00298

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L12
Chain IDs:TA (auth: BL), UA (auth: BM), IB (auth: Bl), JB (auth: Bm), DD (auth: DL), ED (auth: DM), SD (auth: Dl), TD (auth: Dm)
Chain Length:125
Number of Molecules:8
Biological Source:THERMUS THERMOPHILUS

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Gene (Uniprot):rplM
Chain IDs:VA (auth: BN), FD (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60488 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L14
Gene (Uniprot):rplN
Chain IDs:WA (auth: BO), GD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP8 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L15
Gene (Uniprot):rplO
Chain IDs:XA (auth: BP), HD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L16
Gene (Uniprot):rplP
Chain IDs:YA (auth: BQ), ID (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60489 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L17
Gene (Uniprot):rplQ
Chain IDs:ZA (auth: BR), JD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L18
Gene (Uniprot):rplR
Chain IDs:AB (auth: BS), KD (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L19
Gene (Uniprot):rplS
Chain IDs:BB (auth: BT), LD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60490 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L20
Gene (Uniprot):rplT
Chain IDs:CB (auth: BU), MD (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60491 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L21
Gene (Uniprot):rplU
Chain IDs:DB (auth: BV), ND (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60492 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L22
Gene (Uniprot):rplV
Chain IDs:EB (auth: BW), OD (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP3 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L23
Gene (Uniprot):rplW
Chain IDs:FB (auth: BX), PD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L24
Gene (Uniprot):rplX
Chain IDs:GB (auth: BY), QD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP9 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:HB (auth: BZ), RD (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
5MU	V	U	5-METHYLURIDINE 5'-MONOPHOSPHATE

Ligand Molecules

FUA

GDP

Primary Citation

The structure of the ribosome with elongation factor G trapped in the posttranslocational state.

Gao, Y.G, Selmer, M, Dunham, C.M, Weixlbaumer, A, Kelley, A.C, Ramakrishnan, V.Show

Science 326 694 699 (2009)

PMID: 19833919 DOI: 10.1126/science.1179709

Abstact

Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.

Legend

Protein

Chemical

Disease

Primary Citation of related structures