8V87
60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
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) | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 1 | GenBank (2211412803) | Saccharomyces cerevisiae BY4741 | |
| 2 | B (2) | 5.8S ribosomal RNA | polymer | 158 | 50682.9 | 1 | GenBank (1772891209) | Saccharomyces cerevisiae BY4741 | |
| 3 | C (3) | ATP-dependent RNA helicase DBP10 | polymer | 995 | 113126.5 | 1 | UniProt (Q12389) Pfam (PF00270) Pfam (PF00271) Pfam (PF08147) | Saccharomyces cerevisiae BY4741 | |
| 4 | D (6) | ITS2 RNA | polymer | 232 | 74308.4 | 1 | Saccharomyces cerevisiae BY4741 | ||
| 5 | E (7) | 60S ribosomal subunit assembly/export protein LOC1 | polymer | 204 | 23652.6 | 1 | UniProt (P43586) | Saccharomyces cerevisiae BY4741 | Localization of ASH1 mRNA protein 1 |
| 6 | F (8) | Nucleolar complex protein 2 | polymer | 710 | 81719.3 | 1 | UniProt (P39744) Pfam (PF03715) | Saccharomyces cerevisiae BY4741 | |
| 7 | G (A) | Ribosome biogenesis protein BRX1 | polymer | 291 | 33585.4 | 1 | UniProt (Q08235) Pfam (PF04427) | Saccharomyces cerevisiae BY4741 | |
| 8 | H (B) | 60S ribosomal protein L3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) | Saccharomyces cerevisiae BY4741 | 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 BY4741 | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
| 10 | J (D) | ATP-dependent RNA helicase HAS1 | polymer | 505 | 56798.3 | 1 | UniProt (Q03532) Pfam (PF00271) Pfam (PF13959) Pfam (PF00270) | Saccharomyces cerevisiae BY4741 | Helicase associated with SET1 protein 1 |
| 11 | K (E) | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 1 | UniProt (Q02326) Pfam (PF01159) | Saccharomyces cerevisiae BY4741 | 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 BY4741 | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
| 13 | M (G) | Large ribosomal subunit protein eL8A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) | Saccharomyces cerevisiae BY4741 | |
| 14 | N (H) | Large ribosomal subunit protein uL6A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) | Saccharomyces cerevisiae BY4741 | |
| 15 | O (I) | Nucleolar complex-associated protein 3 | polymer | 663 | 75689.0 | 1 | UniProt (Q07896) Pfam (PF07540) Pfam (PF03914) | Saccharomyces cerevisiae BY4741 | |
| 16 | P (J) | rRNA-processing protein EBP2 | polymer | 427 | 49842.6 | 1 | UniProt (P36049) Pfam (PF05890) | Saccharomyces cerevisiae BY4741 | EBNA1-binding protein homolog |
| 17 | Q (K) | Proteasome-interacting protein CIC1 | polymer | 376 | 42596.7 | 1 | UniProt (P38779) Pfam (PF00687) | Saccharomyces cerevisiae BY4741 | |
| 18 | R (L) | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) | Saccharomyces cerevisiae BY4741 | 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 BY4741 | Large ribosomal subunit protein eL14-A |
| 20 | T (N) | Large ribosomal subunit protein eL15A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) | Saccharomyces cerevisiae BY4741 | |
| 21 | U (O) | Large ribosomal subunit protein uL13A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) | Saccharomyces cerevisiae BY4741 | |
| 22 | V (P) | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) | Saccharomyces cerevisiae BY4741 | 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 BY4741 | 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 BY4741 | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
| 25 | Y (S) | Large ribosomal subunit protein eL20A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) | Saccharomyces cerevisiae BY4741 | |
| 26 | Z (U) | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) | Saccharomyces cerevisiae BY4741 | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
| 27 | AA (V) | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) | Saccharomyces cerevisiae BY4741 | L17a,Large ribosomal subunit protein uL14-A,YL32 |
| 28 | BA (W) | Ribosome assembly factor MRT4 | polymer | 236 | 27098.0 | 1 | UniProt (P33201) Pfam (PF00466) Pfam (PF17777) | Saccharomyces cerevisiae BY4741 | |
| 29 | CA (X) | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
| 30 | DA (Y) | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) | Saccharomyces cerevisiae BY4741 | L33,Large ribosomal subunit protein uL24-A,YL33 |
| 31 | EA (Z) | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL27-A |
| 32 | FA (a) | Large ribosomal subunit protein uL1A | polymer | 217 | 24524.8 | 1 | UniProt (P0CX43) Pfam (PF00687) | Saccharomyces cerevisiae BY4741 | |
| 33 | GA (b) | Nucleolar GTP-binding protein 1 | polymer | 647 | 74531.2 | 1 | UniProt (Q02892) Pfam (PF17835) Pfam (PF06858) Pfam (PF08155) | Saccharomyces cerevisiae BY4741 | |
| 34 | HA (c) | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) | Saccharomyces cerevisiae BY4741 | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
| 35 | IA (d) | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) | Saccharomyces cerevisiae BY4741 | L34,Large ribosomal subunit protein eL31-A,YL28 |
| 36 | JA (e) | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL32 |
| 37 | KA (f) | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) | Saccharomyces cerevisiae BY4741 | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
| 38 | LA (g) | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL34-A |
| 39 | MA (h) | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein uL29-A |
| 40 | NA (i) | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) | Saccharomyces cerevisiae BY4741 | L39,Large ribosomal subunit protein eL36-A,YL39 |
| 41 | OA (j) | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) | Saccharomyces cerevisiae BY4741 | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
| 42 | PA (k) | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL38 |
| 43 | QA (l) | 60S ribosome subunit biogenesis protein NIP7 | polymer | 181 | 20411.7 | 1 | UniProt (Q08962) Pfam (PF17833) Pfam (PF03657) | Saccharomyces cerevisiae BY4741 | |
| 44 | RA (m) | Ribosome biogenesis protein ERB1 | polymer | 807 | 91830.6 | 1 | UniProt (Q04660) Pfam (PF08145) Pfam (PF00400) | Saccharomyces cerevisiae BY4741 | Eukaryotic ribosome biogenesis protein 1 |
| 45 | SA (n) | Pescadillo homolog | polymer | 605 | 69984.1 | 1 | UniProt (P53261) Pfam (PF06732) Pfam (PF16589) | Saccharomyces cerevisiae BY4741 | Nucleolar protein 7,Ribosomal RNA-processing protein 13 |
| 46 | TA (o) | Ribosome biogenesis protein 15 | polymer | 220 | 25499.2 | 1 | UniProt (P53927) Pfam (PF00076) | Saccharomyces cerevisiae BY4741 | Nucleolar protein 15 |
| 47 | UA (p) | YTM1 isoform 1 | polymer | 460 | 51426.6 | 1 | UniProt (A0A8H4BV53) Pfam (PF08154) Pfam (PF00400) UniProt (by SIFTS) (Q12024) | Saccharomyces cerevisiae BY4741 | |
| 48 | VA (q) | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | polymer | 618 | 69912.2 | 1 | UniProt (P40991) Pfam (PF01189) | Saccharomyces cerevisiae BY4741 | Nucleolar protein 2 |
| 49 | WA (r) | Ribosome biogenesis protein NSA2 | polymer | 261 | 29786.8 | 1 | UniProt (P40078) Pfam (PF01201) | Saccharomyces cerevisiae BY4741 | NOP7-associated protein 2 |
| 50 | XA (s) | Nuclear GTP-binding protein NUG1 | polymer | 520 | 57798.7 | 1 | UniProt (P40010) Pfam (PF08701) Pfam (PF01926) | Saccharomyces cerevisiae BY4741 | Nuclear GTPase 1 |
| 51 | YA (t) | Ribosome biogenesis protein RLP7 | polymer | 322 | 36621.1 | 1 | UniProt (P40693) Pfam (PF00327) | Saccharomyces cerevisiae BY4741 | Ribosomal protein L7-like |
| 52 | ZA (u) | Ribosome biogenesis protein RLP24 | polymer | 199 | 24027.7 | 1 | UniProt (Q07915) Pfam (PF01246) | Saccharomyces cerevisiae BY4741 | |
| 53 | AB (v) | Nucleolar protein 16 | polymer | 231 | 26954.4 | 1 | UniProt (P40007) Pfam (PF09420) | Saccharomyces cerevisiae BY4741 | |
| 54 | BB (w) | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | polymer | 841 | 96656.2 | 1 | UniProt (P25582) Pfam (PF01728) Pfam (PF11861) Pfam (PF07780) | Saccharomyces cerevisiae BY4741 | 2'-O-ribose RNA methyltransferase SPB1,AdoMet-dependent rRNA methyltransferase SPB1,S-adenosyl-L-methionine-dependent methyltransferase,Suppressor of PAB1 protein 1 |
| 55 | CB (y) | Eukaryotic translation initiation factor 6 | polymer | 245 | 26476.6 | 1 | UniProt (Q12522) Pfam (PF01912) | Saccharomyces cerevisiae BY4741 | eIF-6 |
| 56 | DB (z) | UPF0642 protein YBL028C | polymer | 106 | 12435.4 | 1 | UniProt (P38202) Pfam (PF10338) | Saccharomyces cerevisiae BY4741 | |
| 57 | EB (3) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) | |||
| 58 | FB, IB (3, b) | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) | |||
| 59 | GB (b) | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 1 | Chemie (GDP) | |||
| 60 | HB (b) | POTASSIUM ION | non-polymer | 39.1 | 1 | Chemie (K) | |||
| 61 | JB, KB (g, j) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 56 |
| Total formula weight | 2996631.6 | |
| Non-Polymers* | Number of molecules | 7 |
| Total formula weight | 1088.9 | |
| All* | Total formula weight | 2997720.5 |
