6HCJ image
Deposition Date 2018-08-15
Release Date 2018-10-17
Last Version Date 2024-10-09
Entry Detail
PDB ID:
6HCJ
Keywords:
Title:
Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAs
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.80 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
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:1869
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L8
Gene (Uniprot):RPL8
Chain IDs:LA (auth: A3)
Chain Length:257
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:E (auth: B2)
Chain Length:295
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL3
Gene (Uniprot):RPL3
Chain IDs:MA (auth: B3)
Chain Length:403
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3a
Gene (Uniprot):RPS3A
Chain IDs:F (auth: C2)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL4
Chain IDs:NA (auth: C3)
Chain Length:425
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS5
Chain IDs:G (auth: D2)
Chain Length:293
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:OA (auth: D3)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS3
Gene (Uniprot):RPS3
Chain IDs:H (auth: E2)
Chain Length:243
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:I (auth: F2)
Chain Length:263
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):LOC100341489
Chain IDs:QA (auth: F3)
Chain Length:247
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL8
Chain IDs:RA (auth: G3)
Chain Length:319
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:SA (auth: H3)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:TA (auth: I3)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eS8
Chain IDs:M (auth: J2)
Chain Length:208
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
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
Polymer Type:polypeptide(L)
Molecule:eS10
Chain IDs:O (auth: L2)
Chain Length:165
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL13
Chain IDs:VA (auth: L3)
Chain Length:211
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
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
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
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
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
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
Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:ZA (auth: P3)
Chain Length:92
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:AB (auth: Q3)
Chain Length:188
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL19
Chain IDs:BB (auth: R3)
Chain Length:137
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:CB (auth: S3)
Chain Length:176
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
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
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
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
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
Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:Z (auth: W2)
Chain Length:83
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
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
Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:BA (auth: Y2)
Chain Length:143
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:CA (auth: Z2)
Chain Length:130
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eS25
Gene (Uniprot):RPS25
Chain IDs:DA (auth: a2)
Chain Length:1869
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL15
Gene (Uniprot):RPL27A
Chain IDs:JB (auth: a3)
Chain Length:257
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
Polymer Type:polypeptide(L)
Molecule:eL29
Gene (Uniprot):RPL29
Chain IDs:KB (auth: b3)
Chain Length:403
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):RPS27
Chain IDs:FA (auth: c2)
Chain Length:264
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL30
Gene (Uniprot):RPL30
Chain IDs:LB (auth: c3)
Chain Length:425
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:GA (auth: d2)
Chain Length:293
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):RPL31
Chain IDs:MB (auth: d3)
Chain Length:125
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):RPS29
Chain IDs:HA (auth: e2)
Chain Length:243
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL32
Chain IDs:NB (auth: e3)
Chain Length:291
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):FAU
Chain IDs:IA (auth: f2)
Chain Length:263
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL33
Gene (Uniprot):RPL35A
Chain IDs:OB (auth: f3)
Chain Length:247
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:PB (auth: g3)
Chain Length:319
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):RPL35
Chain IDs:QB (auth: h3)
Chain Length:123
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36
Gene (Uniprot):RPL36
Chain IDs:RB (auth: i3)
Chain Length:214
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polypeptide(L)
Molecule:eL38
Chain IDs:TB (auth: k3)
Chain Length:70
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):LOC100343258
Chain IDs:UB (auth: l3)
Chain Length:211
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
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
Polymer Type:polyribonucleotide
Molecule:A/P RNA
Chain IDs:AC (auth: q3)
Chain Length:188
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:eL28
Gene (Uniprot):RPL28
Chain IDs:ZB (auth: r3)
Chain Length:137
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL10
Chain IDs:BC (auth: t3)
Chain Length:160
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
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
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DC (auth: v3)
Chain Length:22
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Polymer Type:polypeptide(L)
Molecule:uL1
Gene (Uniprot):RPL10A
Chain IDs:FC (auth: w3)
Chain Length:217
Number of Molecules:1
Biological Source:Oryctolagus cuniculus
Primary Citation
ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
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.

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Primary Citation of related structures