ISDA

Deposition Date 2014-10-22

Release Date 2015-01-28

Last Version Date 2024-12-25

Entry Detail

PDB ID:

4WQY

Keywords:

RIBOSOME

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G in the post-translocational state (without fusitic acid)

Biological Source:

Source Organism:

Escherichia coli str. K-12 substr. MC4100 (Taxon ID: 1403831)
Thermus thermophilus (Taxon ID: 300852)
synthetic construct (Taxon ID: 32630)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.26

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:X (auth: A0), CC (auth: C0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:Y (auth: A1), DC (auth: C1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Z (auth: A2), EC (auth: C2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:AA (auth: A3), FC (auth: C3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:BA (auth: A4), GC (auth: C4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:CA (auth: A5), HC (auth: C5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:DA (auth: A6), IC (auth: C6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:EA (auth: A7), JC (auth: C7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:FA (auth: A8), KC (auth: C8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:GA (auth: A9), LC (auth: C9)
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:A (auth: AA), FB (auth: CA)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:B (auth: AB), GB (auth: CB)
Chain Length:121
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:C (auth: AC), HB (auth: CC)
Chain Length:228
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:D (auth: AD), IB (auth: CD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:E (auth: AE), JB (auth: CE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:F (auth: AF), KB (auth: CF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:G (auth: AG), LB (auth: CG)
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:H (auth: AH), MB (auth: CH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:I (auth: AK), NB (auth: CK)
Chain Length:173
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q8VVE3 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:J (auth: AL), OB (auth: CL)
Chain Length:147
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP6 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:K (auth: AN), PB (auth: CN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:L (auth: AO), QB (auth: CO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:M (auth: AP), RB (auth: CP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:N (auth: AQ), SB (auth: CQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:O (auth: AR), TB (auth: CR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:P (auth: AS), UB (auth: CS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:Q (auth: AT), VB (auth: CT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:R (auth: AU), WB (auth: CU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:S (auth: AV), XB (auth: CV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:T (auth: AW), YB (auth: CW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:U (auth: AX), ZB (auth: CX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:V (auth: AY), AC (auth: CY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:W (auth: AZ), BC (auth: CZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:HA (auth: BA), MC (auth: DA)
Chain Length:1521
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:IA (auth: BB), NC (auth: DB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:JA (auth: BC), OC (auth: DC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: BD), PC (auth: DD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: BE), QC (auth: DE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:MA (auth: BF), RC (auth: DF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: BG), SC (auth: DG)
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:OA (auth: BH), TC (auth: DH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: BI), UC (auth: DI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:QA (auth: BJ), VC (auth: DJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:RA (auth: BK), WC (auth: DK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:SA (auth: BL), XC (auth: DL)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:TA (auth: BM), YC (auth: DM)
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:UA (auth: BN), ZC (auth: DN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:VA (auth: BO), AD (auth: DO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:WA (auth: BP), BD (auth: DP)
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:XA (auth: BQ), CD (auth: DQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:YA (auth: BR), DD (auth: DR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:ZA (auth: BS), ED (auth: DS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: BT), FD (auth: DT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:BB (auth: BU), GD (auth: DU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:CB (auth: BV), HD (auth: DV)
Chain Length:24
Number of Molecules:2
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:DB (auth: BX), ID (auth: DX)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MC4100

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9,Elongation factor G
Gene (Uniprot):fusA, rplI
Chain IDs:EB (auth: BZ), JD (auth: DZ)
Chain Length:758
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1,Q5SHN5 Pfam ID:PF01281, PF00009, PF03144, PF14492, PF03764, PF00679

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	DB	U	modified residue
5MC	DB	C	modified residue
5MU	DB	U	modified residue
PSU	DB	U	modified residue

Ligand Molecules

GDP

SF4

Primary Citation

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.

Lin, J, Gagnon, M.G, Bulkley, D, Steitz, T.A.Show

Cell 160 219 227 (2015)

PMID: 25594181 DOI: 10.1016/j.cell.2014.11.049

Abstact

The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.

Legend

Protein

Chemical

Disease

Primary Citation of related structures