ISDA

Deposition Date 2021-08-24

Release Date 2021-11-17

Last Version Date 2025-03-19

Entry Detail

PDB ID:

7PJU

Keywords:

RIBOSOME

Title:

Structure of the 70S ribosome with tRNAs in hybrid state 2 (H2)

Biological Source:

Source Organism:

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

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

9.50 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
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
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:1542
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:I (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
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
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
Chain IDs:L (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P60723

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
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
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
Chain IDs:O (auth: H)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Chain IDs:P (auth: I)
Chain Length:130
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
Chain IDs:Q (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0AA10

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:R (auth: K)
Chain Length:129
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
Chain IDs:S (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P02413

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
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
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
Chain IDs:V (auth: O)
Chain Length:89
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
Chain IDs:W (auth: P)
Chain Length:115
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
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
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:Ribosomal protein L22
Chain IDs:Z (auth: S)
Chain Length:110
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
Chain IDs:AA (auth: T)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L24
Chain IDs:BA (auth: U)
Chain Length:104
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
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
Chain IDs:DA (auth: W)
Chain Length:76
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
Chain IDs:EA (auth: X)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7M2

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:FA (auth: Y)
Chain Length:2
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
Chain IDs:GA (auth: Z)
Chain Length:59
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:1542
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:IA (auth: b)
Chain Length:120
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
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:Ribosomal protein S4
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
Chain IDs:LA (auth: e)
Chain Length:201
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
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
Chain IDs:OA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7W7

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:PA (auth: i)
Chain Length:130
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
Chain IDs:QA (auth: j)
Chain Length:103
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
Chain IDs:RA (auth: k)
Chain Length:129
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
Chain IDs:SA (auth: l)
Chain Length:144
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
Chain IDs:TA (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7S9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
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
Chain IDs:VA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ADZ4

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:WA (auth: p)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0A7T3

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
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
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
Chain IDs:ZA (auth: s)
Chain Length:110
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
Chain IDs:AB (auth: t)
Chain Length:87
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
Chain IDs:BB (auth: u)
Chain Length:104
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:76
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polypeptide(L)
Molecule:Dipeptide (FME-PHE)
Chain IDs:EB (auth: y)
Chain Length:2
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:FB (auth: z)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	CB	U	modified residue
5MU	CB	U	modified residue
H2U	CB	U	modified residue
PSU	CB	U	modified residue

Ligand Molecules

AM2

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