6M62
Cryo-Em structure of eukaryotic pre-60S ribosome subunit from Saccharomyces cerevisiae rpf2 delta 255-344 strain, C4 state.
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 (1) | RDN25-1 rRNA | polymer | 3396 | 1097493.9 | 1 | GenBank (NR_132207) | Saccharomyces cerevisiae S288C | |
| 2 | B (2) | RDN58-1 rRNA | polymer | 158 | 50682.9 | 1 | GenBank (1669301378) | Saccharomyces cerevisiae S288C | |
| 3 | C (3) | RDN5-2 rRNA | polymer | 121 | 38951.1 | 1 | GenBank (1039023795) | Saccharomyces cerevisiae S288C | |
| 4 | D (4) | Probable metalloprotease ARX1 | polymer | 593 | 65290.3 | 1 | UniProt (Q03862) | Saccharomyces cerevisiae S288C (Baker's yeast) | Associated with ribosomal export complex protein 1 |
| 5 | E (5) | rRNA-processing protein CGR1 | polymer | 120 | 14460.1 | 1 | UniProt (P53188) Pfam (PF03879) | Saccharomyces cerevisiae S288c (Baker's yeast) | Coiled-coil growth-regulated protein 1 |
| 6 | F (6) | ITS2-1 miscRNA | polymer | 232 | 74308.4 | 1 | Saccharomyces cerevisiae S288C (Baker's yeast) | ||
| 7 | G (A) | 60S ribosomal protein L2-A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) | Saccharomyces cerevisiae S288c (Baker's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
| 8 | H (B) | 60S ribosomal protein L3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
| 9 | I (C) | 60S ribosomal protein L4-A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) | Saccharomyces cerevisiae S288c (Baker's yeast) | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
| 10 | J (D) | 60S ribosomal protein L5 | polymer | 297 | 33764.8 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) | Saccharomyces cerevisiae S288c (Baker's yeast) | L1,L1a,Ribosomal 5S RNA-binding protein,YL3 |
| 11 | K (E) | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 1 | UniProt (Q02326) Pfam (PF01159) | Saccharomyces cerevisiae S288c (Baker's yeast) | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
| 12 | L (F) | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) | Saccharomyces cerevisiae S288c (Baker's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 13 | M (G) | 60S ribosomal protein L8-A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae S288c (Baker's yeast) | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
| 14 | N (H) | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae S288c (Baker's yeast) | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
| 15 | O (I) | Bud site selection protein 20 | polymer | 166 | 18547.0 | 1 | UniProt (Q08004) Pfam (PF12171) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 16 | P (J) | 60S ribosomal protein L11-A | polymer | 174 | 19755.7 | 1 | UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) | Saccharomyces cerevisiae S288c (Baker's yeast) | L16,RP39,YL22 |
| 17 | Q (K) | Proteasome-interacting protein CIC1 | polymer | 376 | 42596.7 | 1 | UniProt (P38779) Pfam (PF00687) | Saccharomyces cerevisiae S288c (Baker's yeast) | Core interacting component 1 |
| 18 | R (L) | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein eL13-A |
| 19 | S (M) | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein eL14-A |
| 20 | T (N) | 60S ribosomal protein L15-A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) | Saccharomyces cerevisiae S288c (Baker's yeast) | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
| 21 | U (O) | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae S288c (Baker's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
| 22 | V (P) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae S288c (Baker's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
| 23 | W (Q) | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
| 24 | X (R) | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) | Saccharomyces cerevisiae S288c (Baker's yeast) | L23,RP15L,RP33,YL14 |
| 25 | Y (S) | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae S288c (Baker's yeast) | L18a,Large ribosomal subunit protein eL20-A |
| 26 | Z (T) | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 27 | AA (U) | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae S288c (Baker's yeast) | L1c,RP4,YL31 |
| 28 | BA (V) | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae S288c (Baker's yeast) | L17a,YL32 |
| 29 | CA (W) | Ribosome assembly factor MRT4 | polymer | 236 | 27098.0 | 1 | UniProt (P33201) Pfam (PF00466) Pfam (PF17777) | Saccharomyces cerevisiae S288c (Baker's yeast) | mRNA turnover protein 4 |
| 30 | DA (X) | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae S288c (Baker's yeast) | RP16L,YL25,YP42' |
| 31 | EA (Y) | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae S288c (Baker's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 32 | FA (Z) | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 33 | GA (a) | 60S ribosomal protein L28 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) Pfam (PF00828) | Saccharomyces cerevisiae S288c (Baker's yeast) | L27a,L29,RP44,RP62,YL24 |
| 34 | HA (b) | Nucleolar GTP-binding protein 1 | polymer | 647 | 74531.2 | 1 | UniProt (Q02892) Pfam (PF17835) Pfam (PF06858) Pfam (PF08155) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 35 | IA (c) | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae S288c (Baker's yeast) | L32,RP73,YL38 |
| 36 | JA (d) | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae S288c (Baker's yeast) | L34,YL28 |
| 37 | KA (e) | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein eL32 |
| 38 | LA (f) | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae S288c (Baker's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 39 | MA (g) | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 40 | NA (h) | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae S288c (Baker's yeast) | Large ribosomal subunit protein uL29-A |
| 41 | OA (i) | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae S288c (Baker's yeast) | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 42 | PA (j) | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae S288c (Baker's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 43 | QA (k) | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 44 | RA (l) | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) Pfam (PF00832) | Saccharomyces cerevisiae S288c (Baker's yeast) | L46,YL40 |
| 45 | SA (m) | Nucleolar GTP-binding protein 2 | polymer | 486 | 55585.6 | 1 | UniProt (P53742) Pfam (PF08153) Pfam (PF01926) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 46 | TA (n) | Pescadillo homolog | polymer | 605 | 69984.1 | 1 | UniProt (P53261) Pfam (PF06732) Pfam (PF16589) | Saccharomyces cerevisiae S288c (Baker's yeast) | Nucleolar protein 7,Ribosomal RNA-processing protein 13 |
| 47 | UA (o) | Ribosome biogenesis protein 15 | polymer | 220 | 25499.2 | 1 | UniProt (P53927) Pfam (PF00076) | Saccharomyces cerevisiae S288c (Baker's yeast) | Nucleolar protein 15 |
| 48 | VA (p) | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) Pfam (PF01780) | Saccharomyces cerevisiae S288c (Baker's yeast) | L37a,YL35 |
| 49 | WA (q) | Ribosome biogenesis protein NOP53 | polymer | 455 | 52667.8 | 1 | UniProt (Q12080) Pfam (PF07767) | Saccharomyces cerevisiae S288c (Baker's yeast) | Nucleolar protein 53 |
| 50 | XA (r) | Ribosome biogenesis protein NSA2 | polymer | 261 | 29786.8 | 1 | UniProt (P40078) Pfam (PF01201) | Saccharomyces cerevisiae S288c (Baker's yeast) | NOP7-associated protein 2 |
| 51 | YA (s) | Nuclear GTP-binding protein NUG1 | polymer | 520 | 57798.7 | 1 | UniProt (P40010) Pfam (PF08701) Pfam (PF01926) | Saccharomyces cerevisiae S288c (Baker's yeast) | Nuclear GTPase 1 |
| 52 | ZA (t) | Ribosome biogenesis protein RLP7 | polymer | 322 | 36621.1 | 1 | UniProt (P40693) Pfam (PF00327) | Saccharomyces cerevisiae S288c (Baker's yeast) | Ribosomal protein L7-like |
| 53 | AB (u) | Ribosome biogenesis protein RLP24 | polymer | 199 | 24027.7 | 1 | UniProt (Q07915) Pfam (PF01246) | Saccharomyces cerevisiae S288c (Baker's yeast) | Ribosomal protein L24-like |
| 54 | BB (v) | Ribosome biogenesis protein RPF2 | polymer | 254 | 29389.5 | 1 | UniProt (P36160) Pfam (PF04427) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 55 | CB (w) | Regulator of ribosome biosynthesis | polymer | 203 | 23001.4 | 1 | UniProt (Q08746) Pfam (PF04939) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 56 | DB (x) | Ribosome assembly protein 4 | polymer | 515 | 57106.8 | 1 | UniProt (P25382) Pfam (PF08154) Pfam (PF00400) | Saccharomyces cerevisiae S288c (Baker's yeast) | Notchless protein homolog 1,Ribosome biogenesis factor RSA4 |
| 57 | EB (y) | Eukaryotic translation initiation factor 6 | polymer | 245 | 26476.6 | 1 | UniProt (Q12522) Pfam (PF01912) | Saccharomyces cerevisiae S288c (Baker's yeast) | eIF-6 |
| 58 | FB (z) | UPF0642 protein YBL028C | polymer | 106 | 12435.4 | 1 | UniProt (P38202) Pfam (PF10338) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 59 | GB, JB, MB, NB (I, j, p, u) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
| 60 | HB, KB (b, m) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 2 | Chemie (GTP) | |||
| 61 | IB, LB (b, m) | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 58 |
| Total formula weight | 2667997.4 | |
| Non-Polymers* | Number of molecules | 8 |
| Total formula weight | 1356.6 | |
| All* | Total formula weight | 2669354.1 |
