6R84
Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)
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 (A) | ABC transporter ATP-binding protein ARB1 | polymer | 519 | 58604.4 | 1 | UniProt (P40024) Pfam (PF00005) Pfam (PF12848) | Saccharomyces cerevisiae (Baker's yeast) | ATP-binding cassette protein involved in ribosome biogenesis 1 |
| 2 | B (R) | Protein VMS1,Vms1,Protein VMS1,Vms1 | polymer | 433 | 48653.2 | 1 | UniProt (Q04311) Pfam (PF18826) | Saccharomyces cerevisiae (Baker's yeast) | VCP/CDC48-associated mitochondrial stress-responsive protein 1,VCP/CDC48-associated mitochondrial stress-responsive protein 1 |
| 3 | C (X) | Eukaryotic translation initiation factor 6 | polymer | 224 | 24156.2 | 1 | UniProt (Q12522) Pfam (PF01912) | Saccharomyces cerevisiae (Baker's yeast) | eIF-6 |
| 4 | D (i) | 60S ribosomal protein L34-A | polymer | 112 | 12608.8 | 1 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL34-A |
| 5 | E (J) | 60S ribosomal protein L7-A | polymer | 222 | 25240.4 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) | Saccharomyces cerevisiae (Baker's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 6 | F (j) | 60S ribosomal protein L35-A | polymer | 119 | 13811.4 | 1 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL29-A |
| 7 | G (K) | 60S ribosomal protein L8-A | polymer | 233 | 25815.0 | 1 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae (Baker's yeast) | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
| 8 | H (k) | 60S ribosomal protein L36-A | polymer | 99 | 11020.1 | 1 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae (Baker's yeast) | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 9 | I (7) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae (Baker's yeast) | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
| 10 | J (l) | 60S ribosomal protein L37-A | polymer | 87 | 9746.2 | 1 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae (Baker's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 11 | K (M) | 60S ribosomal protein L11-B | polymer | 169 | 19266.1 | 1 | UniProt (Q3E757) Pfam (PF00281) Pfam (PF00673) | Saccharomyces cerevisiae (Baker's yeast) | L16,Large ribosomal subunit protein uL5-B,RP39,YL22 |
| 12 | L (m) | 60S ribosomal protein L38 | polymer | 77 | 8714.4 | 1 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL38 |
| 13 | M (N) | 60S ribosomal protein L13-A | polymer | 193 | 21885.2 | 1 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL13-A |
| 14 | N (n) | 60S ribosomal protein L39 | polymer | 50 | 6227.4 | 1 | UniProt (P04650) Pfam (PF00832) | Saccharomyces cerevisiae (Baker's yeast) | L46,Large ribosomal subunit protein eL39,YL40 |
| 15 | O (O) | 60S ribosomal protein L14-A | polymer | 136 | 14976.8 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL14-A |
| 16 | P (o) | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6032.3 | 1 | UniProt (P0CH08) Pfam (PF01020) | Saccharomyces cerevisiae (Baker's yeast) | |
| 17 | Q (p) | 60S ribosomal protein L15-A | polymer | 203 | 24351.2 | 1 | UniProt (P05748) Pfam (PF00827) | Saccharomyces cerevisiae (Baker's yeast) | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
| 18 | R (Q) | 60S ribosomal protein L16-A | polymer | 197 | 22029.0 | 1 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae (Baker's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 19 | S (5) | 60S ribosomal protein L17-A | polymer | 183 | 20458.3 | 1 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae (Baker's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 20 | T (S) | 60S ribosomal protein L18-A | polymer | 185 | 20478.1 | 1 | UniProt (P0CX49) Pfam (PF17135) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
| 21 | U (s) | 60S ribosomal protein L10 | polymer | 220 | 25279.3 | 1 | UniProt (P41805) Pfam (PF00252) | Saccharomyces cerevisiae (Baker's yeast) | L9,Large ribosomal subunit protein uL16,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein |
| 22 | V (T) | 60S ribosomal protein L19-A | polymer | 152 | 17447.4 | 1 | UniProt (P0CX82) Pfam (PF01280) | Saccharomyces cerevisiae (Baker's yeast) | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 23 | W (U) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae (Baker's yeast) | L18a,Large ribosomal subunit protein eL20-A |
| 24 | X (V) | 60S ribosomal protein L21-A | polymer | 159 | 18148.1 | 1 | UniProt (Q02753) Pfam (PF01157) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL21-A |
| 25 | Y (W) | 60S ribosomal protein L22-A | polymer | 100 | 11263.9 | 1 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae (Baker's yeast) | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 26 | Z (P) | 60S ribosomal protein L12-A | polymer | 155 | 16679.3 | 1 | UniProt (P0CX53) Pfam (PF03946) Pfam (PF00298) | Saccharomyces cerevisiae (Baker's yeast) | L15,Large ribosomal subunit protein uL11-A,YL23 |
| 27 | AA (r) | 60S acidic ribosomal protein P0 | polymer | 197 | 21715.0 | 1 | UniProt (P05317) Pfam (PF00466) Pfam (PF17777) | Saccharomyces cerevisiae (Baker's yeast) | A0,L10e,Large ribosomal subunit protein uL10 |
| 28 | BA (x) | 60S ribosomal protein L23-A | polymer | 136 | 14362.8 | 1 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae (Baker's yeast) | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 29 | CA (3) | 5S rRNA | polymer | 121 | 38951.1 | 1 | GenBank (1329886537) | Saccharomyces cerevisiae | |
| 30 | DA (Y) | 60S ribosomal protein L24-A | polymer | 62 | 7271.6 | 1 | UniProt (P04449) Pfam (PF01246) | Saccharomyces cerevisiae (Baker's yeast) | L30,Large ribosomal subunit protein eL24-A,RP29,YL21 |
| 31 | EA (4) | 5.8S rRNA | polymer | 158 | 50682.9 | 1 | GenBank (1331532632) | Saccharomyces cerevisiae | |
| 32 | FA (Z) | 60S ribosomal protein L25 | polymer | 121 | 13771.2 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 33 | GA (a) | 60S ribosomal protein L26-A | polymer | 126 | 14134.6 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae (Baker's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 34 | HA (B) | tRNA-Ala | polymer | 76 | 24502.5 | 1 | Saccharomyces cerevisiae | ||
| 35 | IA (b) | 60S ribosomal protein L27-A | polymer | 135 | 15437.2 | 1 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL27-A |
| 36 | JA (C) | 60S ribosomal protein L42-A | polymer | 105 | 12115.5 | 1 | UniProt (P0CX27) Pfam (PF00935) | Saccharomyces cerevisiae (Baker's yeast) | L41,Large ribosomal subunit protein eL42-A,YL27,YP44 |
| 37 | KA (c) | 60S ribosomal protein L28 | polymer | 148 | 16630.5 | 1 | UniProt (P02406) Pfam (PF00828) | Saccharomyces cerevisiae (Baker's yeast) | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
| 38 | LA (D) | 60S ribosomal protein L43-A | polymer | 91 | 9981.8 | 1 | UniProt (P0CX25) Pfam (PF01780) | Saccharomyces cerevisiae (Baker's yeast) | L37a,Large ribosomal subunit protein eL43-A,YL35 |
| 39 | MA (d) | 60S ribosomal protein L29 | polymer | 58 | 6560.7 | 1 | UniProt (P05747) Pfam (PF01779) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL29,YL43 |
| 40 | NA (E) | 60S ribosomal protein L2-A | polymer | 252 | 27217.3 | 1 | UniProt (P0CX45) Pfam (PF03947) Pfam (PF00181) | Saccharomyces cerevisiae (Baker's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 41 | OA (e) | 60S ribosomal protein L30 | polymer | 97 | 10558.3 | 1 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae (Baker's yeast) | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 42 | PA (F) | 60S ribosomal protein L3 | polymer | 386 | 43719.6 | 1 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 43 | QA (f) | 60S ribosomal protein L31-A | polymer | 109 | 12649.8 | 1 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae (Baker's yeast) | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 44 | RA (G) | 60S ribosomal protein L4-A | polymer | 361 | 39027.9 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) | Saccharomyces cerevisiae (Baker's yeast) | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
| 45 | SA (g) | 60S ribosomal protein L32 | polymer | 127 | 14478.1 | 1 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae (Baker's yeast) | Large ribosomal subunit protein eL32 |
| 46 | TA (H) | 60S ribosomal protein L5 | polymer | 296 | 33633.6 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) | Saccharomyces cerevisiae (Baker's yeast) | L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3 |
| 47 | UA (h) | 60S ribosomal protein L33-A | polymer | 106 | 12045.9 | 1 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae (Baker's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 48 | VA (I) | 60S ribosomal protein L6-A | polymer | 175 | 19869.4 | 1 | UniProt (Q02326) Pfam (PF01159) | Saccharomyces cerevisiae (Baker's yeast) | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
| 49 | WA (L) | 60S ribosomal protein L1-A | polymer | 204 | 22974.0 | 1 | UniProt (P0CX43) Pfam (PF00687) | Saccharomyces cerevisiae (Baker's yeast) | L10a,Large ribosomal subunit protein uL1-A |
| 50 | XA (1) | 25S rRNA | polymer | 3316 | 1071848.4 | 1 | Saccharomyces cerevisiae | ||
| 51 | YA (R) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) |
Sequence modifications
R: 13 - 105 (UniProt: Q04311)
R: 113 - 173 (PDB: 6R84)
R: 188 - 529 (UniProt: Q04311)
R: 535 - 549 (PDB: 6R84)
| PDB | External Database | Details |
|---|---|---|
| - | Phe 36 | deletion |
| - | Asp 37 | deletion |
| - | Ser 38 | deletion |
| - | Thr 39 | deletion |
| - | Leu 40 | deletion |
| - | Arg 41 | deletion |
| - | Glu 42 | deletion |
| - | Val 43 | deletion |
| - | Glu 44 | deletion |
| - | Val 45 | deletion |
| - | Glu 46 | deletion |
| - | Lys 47 | deletion |
| - | Thr 48 | deletion |
| - | Ser 49 | deletion |
| - | Asp 50 | deletion |
| - | Asn 51 | deletion |
| - | Asp 52 | deletion |
| - | Arg 53 | deletion |
| - | Asn 54 | deletion |
| - | Lys 55 | deletion |
| - | Glu 56 | deletion |
| - | Ser 57 | deletion |
| - | Gly 58 | deletion |
| - | Asp 59 | deletion |
| - | Leu 60 | deletion |
| - | Gln 61 | deletion |
| - | Ile 62 | deletion |
| - | Ala 63 | deletion |
| - | Arg 64 | deletion |
| - | Lys 65 | deletion |
| - | Lys 66 | deletion |
| - | Val 67 | deletion |
| - | Thr 68 | deletion |
| - | Ser 69 | deletion |
| - | Asn 70 | deletion |
| - | Val 71 | deletion |
| - | Met 72 | deletion |
| - | Arg 73 | deletion |
| - | Phe 81 | deletion |
| - | Asp 82 | deletion |
| - | Ser 83 | deletion |
| - | Arg 84 | deletion |
| - | Asn 85 | deletion |
| - | Glu 86 | deletion |
| - | Gln 87 | deletion |
| - | Lys 88 | deletion |
| - | Ala 89 | deletion |
R: 188 - 529 (UniProt: Q04311)
| PDB | External Database | Details |
|---|---|---|
| Ser 187 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 50 |
| Total formula weight | 2079115.7 | |
| Non-Polymers* | Number of molecules | 1 |
| Total formula weight | 65.4 | |
| All* | Total formula weight | 2079181.1 |
