ISDA

Deposition Date 2021-08-24

Release Date 2021-10-20

Last Version Date 2025-03-12

Entry Detail

PDB ID:

7PJY

Keywords:

RIBOSOME

Title:

Structure of the 70S-EF-G-GDP ribosome complex with tRNAs in chimeric state 1 (CHI1-EF-G-GDP)

Biological Source:

Source Organism:

Escherichia coli (strain K12) (Taxon ID: 83333)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N4 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:B (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:C (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7P5 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:D (auth: 3)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7Q6 Pfam ID:PF00444

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:F (auth: 5)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J3 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:G (auth: 6)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M9 Pfam ID:PF01197

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:H (auth: A)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:I (auth: B)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:J (auth: C)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:K (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:L (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:M (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:N (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG55 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:O (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:P (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:Q (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AA10 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:R (auth: K)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY3 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:S (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02413 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:T (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADY7 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:U (auth: N)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG44 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:V (auth: O)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:W (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:X (auth: Q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Y (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG48 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Z (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P61175 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:AA (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:BA (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:CA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68919 Pfam ID:PF01386

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:DA (auth: W)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:EA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M2 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:FA (auth: Y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:GA (auth: Z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG51 Pfam ID:PF00327

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:HA (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:IA (auth: b)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:JA (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:KA (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:LA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:MA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:NA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:OA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:PA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:QA (auth: j)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:RA (auth: k)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:SA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:TA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S9 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:UA (auth: n)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG59 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:VA (auth: o)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ4 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:WA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:XA (auth: q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AG63 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:YA (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T7 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:ZA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:AB (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7U7 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:BB (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P68679 Pfam ID:PF01165

Polymer Type:polyribonucleotide
Molecule:P-site tRNA(fMet)
Chain IDs:CB (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:P-site fMet-Phe-tRNA(Phe)
Chain IDs:DB (auth: w)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor G
Gene (Uniprot):fusA
Chain IDs:EB (auth: x)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A6M8 Pfam ID:PF00009, PF03144, PF14492, PF03764, PF00679 EC:3.6.5.3

Polymer Type:polypeptide(L)
Molecule:Dipeptide (FME-PHE)
Chain IDs:FB (auth: y)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:GB (auth: z)
Chain Length:33
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
2MG	HA	G	modified residue
4OC	HA	C	modified residue
4SU	CB	U	modified residue
5MC	HA	C	modified residue
5MU	CB	U	modified residue
G7M	HA	G	modified residue
MA6	HA	A	modified residue
PSU	HA	U	modified residue
U	CB	U	modified residue
UR3	HA	U	modified residue

Ligand Molecules

AM2

GDP

Primary Citation

Structural mechanism of GTPase-powered ribosome-tRNA movement.

Petrychenko, V, Peng, B.Z, de A P Schwarzer, A.C, Peske, F, Rodnina, M.V, Fischer, N.Show

Nat Commun 12 5933 5933 (2021)

PMID: 34635670 DOI: 10.1038/s41467-021-26133-x

Abstact

GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP-Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.

Legend

Protein

Chemical

Disease

Primary Citation of related structures