ISDA

Deposition Date 2018-08-16

Release Date 2018-10-17

Last Version Date 2024-11-06

Entry Detail

PDB ID:

6HCQ

Keywords:

RIBOSOME

Title:

Structure of the rabbit collided di-ribosome (collided monosome)

Biological Source:

Source Organism:

Oryctolagus cuniculus (Taxon ID: 9986)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

6.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:nascent chain
Chain IDs:GC (auth: 1)
Chain Length:22
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:P/E tRNA
Chain IDs:EC (auth: 33)
Chain Length:75
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:A (auth: 51)
Chain Length:3635
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 71)
Chain Length:120
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:C (auth: 81)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:D (auth: A2)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:LA (auth: A3)
Chain Length:148
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TT27 Pfam ID:PF00181, PF03947

Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:E (auth: B2)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL3
Gene (Uniprot):RPL3
Chain IDs:MA (auth: B3)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TL06 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:F (auth: C2)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SS70 Pfam ID:PF01015

Polymer Type:polypeptide(L)
Molecule:uL4
Chain IDs:NA (auth: C3)
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:eS1
Chain IDs:G (auth: D2)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:OA (auth: D3)
Chain Length:297
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:P19949

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS3
Gene (Uniprot):RPS3
Chain IDs:H (auth: E2)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TNM3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:PA (auth: E3)
Chain Length:291
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SKF7 Pfam ID:PF03868, PF01159

Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:I (auth: F2)
Chain Length:133
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):LOC100341489
Chain IDs:QA (auth: F3)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TUB1 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:J (auth: G2)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TFM5 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:eL8
Chain IDs:RA (auth: G3)
Chain Length:319
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:K (auth: H2)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TM55 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:SA (auth: H3)
Chain Length:192
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SWI6 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):RPS7
Chain IDs:L (auth: I2)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SVB0

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:TA (auth: I3)
Chain Length:105
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:B7NZQ2 Pfam ID:PF00252

Polymer Type:polypeptide(L)
Molecule:eS8
Chain IDs:M (auth: J2)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:UA (auth: J3)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TUB8 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S9 (Predicted)
Gene (Uniprot):RPS9
Chain IDs:N (auth: K2)
Chain Length:194
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:B7NZS8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:O (auth: L2)
Chain Length:165
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TPV3 Pfam ID:PF03501

Polymer Type:polypeptide(L)
Molecule:eL13
Chain IDs:VA (auth: L3)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S11
Gene (Uniprot):RPS11
Chain IDs:P (auth: M2)
Chain Length:158
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TRM4 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:WA (auth: M3)
Chain Length:218
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SZ12 Pfam ID:PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):RPS12
Chain IDs:Q (auth: N2)
Chain Length:132
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SFR8 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L15
Gene (Uniprot):RPL15
Chain IDs:XA (auth: N3)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1T0C1 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS15
Gene (Uniprot):RPS13
Chain IDs:R (auth: O2)
Chain Length:151
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SP51 Pfam ID:PF08069, PF00312

Polymer Type:polypeptide(L)
Molecule:uL13
Chain IDs:YA (auth: O3)
Chain Length:106
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:uS11
Chain IDs:S (auth: P2)
Chain Length:168
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:ZA (auth: P3)
Chain Length:92
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SCJ6 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS19
Gene (Uniprot):RPS15
Chain IDs:T (auth: Q2)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1U0Q2 Pfam ID:PF00203

Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:AB (auth: Q3)
Chain Length:74
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:U (auth: R2)
Chain Length:146
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SGX4 Pfam ID:PF00380

Polymer Type:polypeptide(L)
Molecule:eL19
Chain IDs:BB (auth: R3)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS17
Gene (Uniprot):RPS17
Chain IDs:V (auth: S2)
Chain Length:135
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TU13 Pfam ID:PF00833

Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:CB (auth: S3)
Chain Length:176
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS13
Gene (Uniprot):RPS18
Chain IDs:W (auth: T2)
Chain Length:152
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TPG3 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL21
Gene (Uniprot):RPL21
Chain IDs:DB (auth: T3)
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SHQ2 Pfam ID:PF01157

Polymer Type:polypeptide(L)
Molecule:eS19
Chain IDs:X (auth: U2)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:eL22
Chain IDs:EB (auth: U3)
Chain Length:165
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS10
Gene (Uniprot):RPS20
Chain IDs:Y (auth: V2)
Chain Length:119
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SIZ2 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:FB (auth: V3)
Chain Length:22
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1T6D1 Pfam ID:PF00238

Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:Z (auth: W2)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S15a
Gene (Uniprot):RPS15A
Chain IDs:AA (auth: X2)
Chain Length:130
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TG89 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23
Gene (Uniprot):RPL23A
Chain IDs:GB (auth: X3)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SE76 Pfam ID:PF03939, PF00276

Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:BA (auth: Y2)
Chain Length:143
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L26
Gene (Uniprot):RPL26
Chain IDs:HB (auth: Y3)
Chain Length:145
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SQH0 Pfam ID:PF16906, PF00467

Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:CA (auth: Z2)
Chain Length:130
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27
Gene (Uniprot):RPL27
Chain IDs:IB (auth: Z3)
Chain Length:136
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TXF6 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS25
Gene (Uniprot):RPS25
Chain IDs:DA (auth: a2)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TDB3 Pfam ID:PF03297

Polymer Type:polypeptide(L)
Molecule:uL15
Chain IDs:JB (auth: a3)
Chain Length:148
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:eS26
Chain IDs:EA (auth: b2)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL29
Gene (Uniprot):RPL29
Chain IDs:KB (auth: b3)
Chain Length:245
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SGR6 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:FA (auth: c2)
Chain Length:84
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TZ76 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL30
Gene (Uniprot):RPL30
Chain IDs:LB (auth: c3)
Chain Length:115
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TDL2 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:GA (auth: d2)
Chain Length:69
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TIB4 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):RPL31
Chain IDs:MB (auth: d3)
Chain Length:297
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SHG0 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):RPS29
Chain IDs:HA (auth: e2)
Chain Length:56
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1U7M4 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL32
Chain IDs:NB (auth: e3)
Chain Length:291
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TUN8 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:IA (auth: f2)
Chain Length:133
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1T8A2 Pfam ID:PF00240, PF04758

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL33
Gene (Uniprot):RPL35A
Chain IDs:OB (auth: f3)
Chain Length:110
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SF08 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S27a
Gene (Uniprot):RPS27A
Chain IDs:JA (auth: g2)
Chain Length:156
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SK22 Pfam ID:PF00240, PF01599

Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:PB (auth: g3)
Chain Length:319
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RACK1
Gene (Uniprot):RACK1
Chain IDs:KA (auth: h2)
Chain Length:317
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SJB4 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):RPL35
Chain IDs:QB (auth: h3)
Chain Length:192
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SIT5 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:RB (auth: i3)
Chain Length:105
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TTQ5 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L37
Gene (Uniprot):RPL37
Chain IDs:SB (auth: j3)
Chain Length:178
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:U3KPD5 Pfam ID:PF01907

Polymer Type:polypeptide(L)
Molecule:eL38
Chain IDs:TB (auth: k3)
Chain Length:70
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):LOC100343258
Chain IDs:UB (auth: l3)
Chain Length:51
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1TTN1 Pfam ID:PF00832

Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:VB (auth: m3)
Chain Length:218
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:eL41
Chain IDs:WB (auth: n3)
Chain Length:204
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Polymer Type:polypeptide(L)
Molecule:eL42
Chain IDs:XB (auth: o3)
Chain Length:106
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL43
Gene (Uniprot):RPL37A
Chain IDs:YB (auth: p3)
Chain Length:92
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SY53 Pfam ID:PF01780

Polymer Type:polyribonucleotide
Molecule:A/P tRNA
Chain IDs:AC (auth: q3)
Chain Length:74
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL28
Gene (Uniprot):RPL28
Chain IDs:ZB (auth: r3)
Chain Length:196
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1U7L1 Pfam ID:PF01778

Polymer Type:polypeptide(L)
Molecule:uL10
Chain IDs:BC (auth: t3)
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:CC (auth: u3)
Chain Length:165
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SMR7 Pfam ID:PF03946, PF00298

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DC (auth: v3)
Chain Length:22
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosomal protein
Gene (Uniprot):RPL10A
Chain IDs:FC (auth: w3)
Chain Length:217
Number of Molecules:1
Biological Source:Oryctolagus cuniculus

UniProt ID:G1SKZ8 Pfam ID:PF00687

Ligand Molecules

Primary Citation

ZNF598 Is a Quality Control Sensor of Collided Ribosomes.

Juszkiewicz, S, Chandrasekaran, V, Lin, Z, Kraatz, S, Ramakrishnan, V, Hegde, R.S.Show

Mol. Cell 72 469 481.e7 (2018)

PMID: 30293783 DOI: 10.1016/j.molcel.2018.08.037

Abstact

Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.

Legend

Protein

Chemical

Disease

Primary Citation of related structures