9OFV
Consensus reconstruction of the eukaryotic Ribosome-associated Quality Control complex
This is a non-PDB format compatible entry.
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B, C, D, E... (A, B, C, D, E...) | Cell division control protein 48 | polymer | 835 | 92105.9 | 6 | UniProt (P25694) Pfam (PF02359) Pfam (PF02933) Pfam (PF00004) Pfam (PF17862) | Saccharomyces cerevisiae (brewer's yeast) | Cell division cycle protein 48, Transitional endoplasmic reticulum ATPase homolog, Cdc48 |
| 2 | G, H, I (K, H, J) | Ubiquitin | polymer | 76 | 8568.8 | 3 | UniProt (P0CG63) Pfam (PF00240) | Saccharomyces cerevisiae (brewer's yeast) | |
| 3 | J (G) | Nuclear protein localization protein 4 | polymer | 580 | 65862.1 | 1 | UniProt (P33755) Pfam (PF05020) Pfam (PF05021) | Saccharomyces cerevisiae (brewer's yeast) | HMG-CoA reductase degradation protein 4, Npl4 |
| 4 | K (3) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae (brewer's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 5 | L (4) | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
| 6 | M (5) | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) Pfam (PF25476) | Saccharomyces cerevisiae (brewer's yeast) | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 7 | N (6) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae (brewer's yeast) | L18a,Large ribosomal subunit protein eL20-A |
| 8 | O (7) | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL21-A |
| 9 | P (8) | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae (brewer's yeast) | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 10 | Q (I) | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae (brewer's yeast) | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 11 | R (9) | Large ribosomal subunit protein eL24A | polymer | 155 | 17661.7 | 1 | UniProt (P04449) Pfam (PF01246) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L24-A,L30,RP29,YL21 |
| 12 | S (L) | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae (brewer's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 13 | T (M) | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL27-A |
| 14 | U (N) | 60S ribosomal protein L28 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) Pfam (PF00828) | Saccharomyces cerevisiae (brewer's yeast) | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
| 15 | V (O) | Large ribosomal subunit protein eL29 | polymer | 59 | 6691.9 | 1 | UniProt (P05747) Pfam (PF01779) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L29,YL43 |
| 16 | W (P) | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae (brewer's yeast) | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 17 | X (Q) | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae (brewer's yeast) | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 18 | Y (R) | Large ribosomal subunit protein eL32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L32 |
| 19 | Z (S) | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae (brewer's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 20 | AA (T) | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL34-A |
| 21 | BA (U) | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein uL29-A |
| 22 | CA (V) | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae (brewer's yeast) | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 23 | DA (W) | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae (brewer's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 24 | EA (Y) | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) Pfam (PF00832) | Saccharomyces cerevisiae (brewer's yeast) | L46,Large ribosomal subunit protein eL39,YL40 |
| 25 | FA (Z) | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14583.1 | 1 | UniProt (P0CH08) Pfam (PF00240) Pfam (PF01020) | Saccharomyces cerevisiae (brewer's yeast) | |
| 26 | GA (b) | 60S ribosomal protein L42-A | polymer | 106 | 12246.7 | 1 | UniProt (P0CX27) Pfam (PF00935) | Saccharomyces cerevisiae (brewer's yeast) | L41,Large ribosomal subunit protein eL42-A,YL27,YP44 |
| 27 | HA (c) | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) Pfam (PF01780) | Saccharomyces cerevisiae (brewer's yeast) | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 28 | IA (d) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 1 | UniProt (P0CX86) Pfam (PF05162) | Saccharomyces cerevisiae (brewer's yeast) | L47,Large ribosomal subunit protein eL41-A,YL41 |
| 29 | JA (f) | 25S rRNA | polymer | 3395 | 1097086.5 | 1 | GenBank (1262303) | Saccharomyces cerevisiae (brewer's yeast) | |
| 30 | KA (h) | 5S rRNA | polymer | 121 | 38951.1 | 1 | GenBank (1039024045) | Saccharomyces cerevisiae (brewer's yeast) | |
| 31 | LA (i) | 5.8S rRNA | polymer | 158 | 50682.9 | 1 | GenBank (1102645687) | Saccharomyces cerevisiae (brewer's yeast) | |
| 32 | MA (j) | 60S ribosomal protein L2-A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) | Saccharomyces cerevisiae (brewer's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 33 | NA (k) | Large ribosomal subunit protein uL3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 34 | OA (l) | Large ribosomal subunit protein uL4A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L4-A,L2,RP2,YL2 |
| 35 | PA (m) | Large ribosomal subunit protein uL18 | polymer | 297 | 33764.8 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L5,L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
| 36 | QA (n) | Large ribosomal subunit protein eL6B | polymer | 176 | 20024.5 | 1 | UniProt (P05739) Pfam (PF01159) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L6-B,L17,RP18,YL16 |
| 37 | RA (o) | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) | Saccharomyces cerevisiae (brewer's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 38 | SA (p) | 60S ribosomal protein L8-A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae (brewer's yeast) | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
| 39 | TA (q) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae (brewer's yeast) | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
| 40 | UA (r) | Large ribosomal subunit protein uL16 | polymer | 221 | 25410.5 | 1 | UniProt (P41805) Pfam (PF00252) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L10,L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 41 | VA (s) | Large ribosomal subunit protein uL5A | polymer | 174 | 19755.7 | 1 | UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L11-A,L16,RP39,YL22 |
| 42 | WA (t) | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL13-A |
| 43 | XA (u) | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein eL14-A |
| 44 | YA (a) | Ribosome quality control complex subunit 2 | polymer | 1038 | 119250.2 | 1 | UniProt (Q12532) Pfam (PF05833) Pfam (PF05670) Pfam (PF11923) | Saccharomyces cerevisiae (brewer's yeast) | Translation-associated element 2 |
| 45 | ZA (e) | E3 ubiquitin-protein ligase listerin | polymer | 1562 | 180373.0 | 1 | UniProt (Q04781) Pfam (PF22958) Pfam (PF22999) Pfam (PF23009) Pfam (PF13639) | Saccharomyces cerevisiae (brewer's yeast) | RING domain mutant killed by rtf1 deletion protein 1,RING-type E3 ubiquitin transferase listerin |
| 46 | AB (g) | Eukaryotic translation initiation factor 6 | polymer | 245 | 26476.6 | 1 | UniProt (Q12522) Pfam (PF01912) | Saccharomyces cerevisiae (brewer's yeast) | eIF-6 |
| 47 | BB, CB (x, y) | Ala tRNA | polymer | 76 | 24502.5 | 2 | Saccharomyces cerevisiae | ||
| 48 | DB (z) | Large ribosomal subunit protein uL11A | polymer | 165 | 17850.6 | 1 | UniProt (P0CX53) Pfam (PF03946) Pfam (PF00298) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L12-A,L15,YL23 |
| 49 | EB (0) | 60S acidic ribosomal protein P0 | polymer | 312 | 33749.1 | 1 | UniProt (P05317) Pfam (PF00466) Pfam (PF17777) Pfam (PF00428) | Saccharomyces cerevisiae (brewer's yeast) | A0,L10e,Large ribosomal subunit protein uL10 |
| 50 | FB (1) | CAT-tailed nascent peptide | polymer | 17 | 1464.8 | 1 | Saccharomyces cerevisiae | ||
| 51 | GB (w) | Large ribosomal subunit protein uL1A | polymer | 217 | 24524.8 | 1 | UniProt (P0CX43) Pfam (PF00687) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L1-A,L10a |
| 52 | HB (X) | Large ribosomal subunit protein eL38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae (brewer's yeast) | 60S ribosomal protein L38 |
| 53 | IB (v) | Ribosome quality control complex subunit 1 | polymer | 753 | 87005.2 | 1 | UniProt (Q05468) Pfam (PF04910) | Saccharomyces cerevisiae (brewer's yeast) | |
| 54 | JB (2) | Polyubiquitin-C | polymer | 76 | 8576.8 | 1 | UniProt (P0CG64) Pfam (PF00240) UniProt (by SIFTS) (P0CG48) | Saccharomyces cerevisiae (brewer's yeast) | |
| 55 | KB (a0) | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae (brewer's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 56 | LB (b0) | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae (brewer's yeast) | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 57 | MB, NB, OB, PB, QB... (A, B, C, D, E...) | ADENOSINE-5'-TRIPHOSPHATE | non-polymer | 507.2 | 9 | Chemie (ATP) | |||
| 58 | TB (E) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) | |||
| 59 | CC, EC, FC, GC, HC... (T, W, Z, b, c...) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 60 | AC, BC, DC, JC, KC... (I, R, T, f, h...) | MAGNESIUM ION | non-polymer | 24.3 | 12 | Chemie (MG) | |||
| 61 | IC (f) | SPERMIDINE | non-polymer | 145.2 | 1 | Chemie (SPD) |
Sequence modifications
A, B, C, D, E, F: 1 - 835 (UniProt: P25694)
f: 1 - 3396 (GenBank: 1262303)
v: 1 - 723 (UniProt: Q05468)
| PDB | External Database | Details |
|---|---|---|
| Gln 588 | Glu 588 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | G 25080 | deletion |
| U 1956 | - | insertion |
| - | A 23482 | deletion |
| U 2255 | - | insertion |
| - | G 23314 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Thr 724 | - | expression tag |
| Ser 725 | - | expression tag |
| Gly 726 | - | expression tag |
| Ser 727 | - | expression tag |
| Pro 728 | - | expression tag |
| Gly 729 | - | expression tag |
| Asp 730 | - | expression tag |
| Tyr 731 | - | expression tag |
| Lys 732 | - | expression tag |
| Asp 733 | - | expression tag |
| Asp 734 | - | expression tag |
| Asp 735 | - | expression tag |
| Asp 736 | - | expression tag |
| Lys 737 | - | expression tag |
| Asp 738 | - | expression tag |
| Tyr 739 | - | expression tag |
| Lys 740 | - | expression tag |
| Asp 741 | - | expression tag |
| Asp 742 | - | expression tag |
| Asp 743 | - | expression tag |
| Asp 744 | - | expression tag |
| Lys 745 | - | expression tag |
| Asp 746 | - | expression tag |
| Tyr 747 | - | expression tag |
| Lys 748 | - | expression tag |
| Asp 749 | - | expression tag |
| Asp 750 | - | expression tag |
| Asp 751 | - | expression tag |
| Asp 752 | - | expression tag |
| Lys 753 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 64 |
| Total formula weight | 3098347.5 | |
| Non-Polymers* | Number of molecules | 30 |
| Total formula weight | 5886.6 | |
| All* | Total formula weight | 3104234.1 |
