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