ISDA

Deposition Date 2017-08-21

Release Date 2018-02-14

Last Version Date 2025-04-09

Entry Detail

PDB ID:

5OT7

Keywords:

RIBOSOME

Title:

Elongation factor G-ribosome complex captures in the absence of inhibitors.

Biological Source:

Source Organism:

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Escherichia coli (Taxon ID: 562)

Host Organism:

Escherichia coli BL21(DE3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:1507
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Polymer Type:polyribonucleotide
Molecule:tRNA-Phe
Chain IDs:B (auth: 2)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:C (auth: 3)
Chain Length:15
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:D (auth: 4)
Chain Length:2901
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:E (auth: 5)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:F (auth: 6)
Chain Length:178
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:G (auth: 7)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:H (auth: A)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:I (auth: B)
Chain Length:50
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:J (auth: C)
Chain Length:48
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:K (auth: D)
Chain Length:151
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:L (auth: E)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:M (auth: F)
Chain Length:227
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:N (auth: G)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:O (auth: H)
Chain Length:205
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:P (auth: I)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:Q (auth: J)
Chain Length:179
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:R (auth: K)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:S (auth: L)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:T (auth: M)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:U (auth: N)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:V (auth: O)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SJH3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:W (auth: P)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P0DOY7 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:X (auth: Q)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:Y (auth: R)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:Z (auth: S)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:AA (auth: T)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SIH3 Pfam ID:PF17070

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Gene (Uniprot):fusA
Chain IDs:BA (auth: U)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:CA (auth: V)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:DA (auth: W)
Chain Length:94
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:EA (auth: X)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:FA (auth: Y)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:GA (auth: Z)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:HA (auth: a)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:IA (auth: b)
Chain Length:50
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:JA (auth: c)
Chain Length:48
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:KA (auth: d)
Chain Length:151
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:LA (auth: e)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHR2 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:MA (auth: f)
Chain Length:227
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:NA (auth: g)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:OA (auth: h)
Chain Length:205
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:PA (auth: i)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:QA (auth: j)
Chain Length:179
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:RA (auth: k)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P0DOY8 Pfam ID:PF00347

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL10
Chain IDs:SA (auth: l)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein uL11
Chain IDs:TA (auth: m)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein bL12
Chain IDs:UA (auth: n)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:VA (auth: o)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:WA (auth: p)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:XA (auth: q)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:YA (auth: r)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:ZA (auth: s)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:AB (auth: t)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:BB (auth: u)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:CB (auth: v)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:DB (auth: w)
Chain Length:94
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:EB (auth: x)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:FB (auth: y)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:GB (auth: z)
Chain Length:71
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Ligand Molecules

GDP

Primary Citation

The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors.

Mace, K, Giudice, E, Chat, S, Gillet, R.Show

Nucleic Acids Res. 46 3211 3217 (2018)

PMID: 29408956 DOI: 10.1093/nar/gky081

Abstact

During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis.

Legend

Protein

Chemical

Disease

Primary Citation of related structures