ISDA: 5U9F

Deposition Date 2016-12-16

Release Date 2017-03-22

Last Version Date 2024-03-13

Entry Detail

PDB ID:

5U9F

Keywords:

RIBOSOME

Title:

3.2 A cryo-EM ArfA-RF2 ribosome rescue complex (Structure II)

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 83333)
Escherichia coli (Taxon ID: 562)

Host Organism:

Escherichia coli K-12

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.20 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:B (auth: 01)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:C (auth: 02)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:F (auth: 03)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L0 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:G (auth: 04)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60422 Pfam ID:PF03947, PF00181

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:H (auth: 05)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:I (auth: 06)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:J (auth: 07)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00673, PF00281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:K (auth: 08)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:L (auth: 09)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF03948, PF01281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Chain IDs:M (auth: 10)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7J3 Pfam ID:PF00466

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:N (auth: 11)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:O (auth: 12)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:P (auth: 13)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:Q (auth: 14)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:R (auth: 15)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:S (auth: 16)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:T (auth: 17)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:U (auth: 18)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:V (auth: 19)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:W (auth: 20)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:X (auth: 21)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:Y (auth: 22)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:Z (auth: 23)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:AA (auth: 24)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:BA (auth: 25)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:CA (auth: 26)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:DA (auth: 27)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:EA (auth: 28)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:FA (auth: 29)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M9 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:GA (auth: 30)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:HA (auth: 31)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:IA (auth: 32)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:JA (auth: 33)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:KA (auth: 34)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1539
Number of Molecules:1
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:OA (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:PA (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF00189, PF07650

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:QA (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:RA (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:SA (auth: F)
Chain Length:131
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:TA (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:UA (auth: H)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:VA (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:WA (auth: J)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:XA (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:YA (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:ZA (auth: M)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:AB (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:BB (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:CB (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:DB (auth: Q)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:EB (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:FB (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:GB (auth: T)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:HB (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Polymer Type:polyribonucleotide
Molecule:truncated mRNA
Chain IDs:LA (auth: V)
Chain Length:14
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:fMet-tRNA (P- and E-site)
Chain IDs:E (auth: X), MA (auth: W)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Alternative ribosome-rescue factor A
Gene (Uniprot):arfA
Chain IDs:D (auth: Y)
Chain Length:72
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P36675 Pfam ID:PF03889

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor RF2
Gene (Uniprot):prfB
Chain IDs:NA (auth: Z)
Chain Length:365
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P07012 Pfam ID:PF03462, PF00472

Ligand Molecules

Primary Citation

Mechanism of ribosome rescue by ArfA and RF2.

Demo, G, Svidritskiy, E, Madireddy, R, Diaz-Avalos, R, Grant, T, Grigorieff, N, Sousa, D, Korostelev, A.A.Show

Elife 6 ? ? (2017)

PMID: 28300532 DOI: 10.7554/eLife.23687

Abstact

ArfA rescues ribosomes stalled on truncated mRNAs by recruiting release factor RF2, which normally binds stop codons to catalyze peptide release. We report two 3.2 Å resolution cryo-EM structures - determined from a single sample - of the 70S ribosome with ArfA•RF2 in the A site. In both states, the ArfA C-terminus occupies the mRNA tunnel downstream of the A site. One state contains a compact inactive RF2 conformation. Ordering of the ArfA N-terminus in the second state rearranges RF2 into an extended conformation that docks the catalytic GGQ motif into the peptidyl-transferase center. Our work thus reveals the structural dynamics of ribosome rescue. The structures demonstrate how ArfA 'senses' the vacant mRNA tunnel and activates RF2 to mediate peptide release without a stop codon, allowing stalled ribosomes to be recycled.

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Protein

Chemical

Disease

Primary Citation of related structures