7D5T
Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1)
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 (3A) | U3 snoRNA | polymer | 333 | 106503.3 | 1 | Saccharomyces cerevisiae S288C | ||
| 2 | B (5A) | 5' ETS | polymer | 700 | 225543.1 | 1 | Saccharomyces cerevisiae S288C | ||
| 3 | C (SA) | 18S rRNA | polymer | 1812 | 583714.6 | 1 | Saccharomyces cerevisiae S288C | ||
| 4 | D (SC) | 40S ribosomal protein S1-A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP10A |
| 5 | E (SF) | 40S ribosomal protein S4-A | polymer | 261 | 29469.3 | 1 | UniProt (P0CX35) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP5,S7,YS6 |
| 6 | F (SG) | 40S ribosomal protein S5 | polymer | 225 | 25072.6 | 1 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP14,S2,YS8 |
| 7 | G (SH) | 40S ribosomal protein S6-A | polymer | 236 | 27054.5 | 1 | UniProt (P0CX37) Pfam (PF01092) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP9,S10,YS4 |
| 8 | H (SI) | 40S ribosomal protein S7-A | polymer | 190 | 21658.2 | 1 | UniProt (P26786) Pfam (PF01251) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP30,RP40 |
| 9 | I (SJ) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 1 | UniProt (P0CX39) Pfam (PF01201) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP19,S14,YS9 |
| 10 | J (SK) | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP21,S13,YP28,YS11 |
| 11 | K (SM) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP41,S18,YS12 |
| 12 | L (SO) | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps13, S27a,YS15 |
| 13 | M (SP) | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps14, RP59A |
| 14 | N (SR) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps16, RP61R |
| 15 | O (SX) | 40S ribosomal protein S22-B | polymer | 130 | 14650.1 | 1 | UniProt (Q3E7Y3) Pfam (PF00410) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps22, RP50,S24,Small ribosomal subunit protein uS8-B,YP58,YS22 |
| 16 | P (SY) | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) Pfam (PF00164) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps23, RP37,S28,YS14 |
| 17 | Q (SZ) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps24,RP50 |
| 18 | R (Sc) | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps27, RP61,YS20 |
| 19 | S (Sd) | 40S ribosomal protein S28-A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps28, S33,YS27 |
| 20 | T, U (3B, 3C) | rRNA 2'-O-methyltransferase fibrillarin | polymer | 327 | 34525.4 | 2 | UniProt (P15646) Pfam (PF01269) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nop1, Histone-glutamine methyltransferase,U3 small nucleolar RNA-associated protein NOP1,U3 snoRNA-associated protein NOP1 |
| 21 | V (3D) | Nucleolar protein 56 | polymer | 504 | 56961.2 | 1 | UniProt (Q12460) Pfam (PF01798) Pfam (PF08156) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nop56, Ribosome biosynthesis protein SIK1,Suppressor of I kappa b protein 1 |
| 22 | W (3E) | Nucleolar protein 58 | polymer | 511 | 57060.3 | 1 | UniProt (Q12499) Pfam (PF08156) Pfam (PF01798) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nucleolar protein 5 |
| 23 | X (3F) | Ribosomal RNA-processing protein 9 | polymer | 573 | 65147.0 | 1 | UniProt (Q06506) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rrp9 |
| 24 | Y, Z (3G, 3H) | 13 kDa ribonucleoprotein-associated protein | polymer | 126 | 13582.9 | 2 | UniProt (P39990) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Snu13, Small nuclear ribonucleoprotein-associated protein 1 |
| 25 | AA (A5) | U3 small nucleolar RNA-associated protein 5 | polymer | 643 | 72079.4 | 1 | UniProt (Q04177) Pfam (PF04003) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp5, U3 snoRNA-associated protein 5,U three protein 5,U3 protein 5 required for transcription,t-UTP5 |
| 26 | BA (AE) | U3 small nucleolar RNA-associated protein 10 | polymer | 1769 | 200299.0 | 1 | UniProt (P42945) Pfam (PF12397) Pfam (PF08146) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp10, U3 snoRNA-associated protein 10,U three protein 10,U3 protein 10 required for transcription,t-UTP10 |
| 27 | CA (AG) | NET1-associated nuclear protein 1 | polymer | 896 | 101341.7 | 1 | UniProt (Q02931) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp17, U three protein 17,t-17,U3 protein 17 required for transcription,U3 small nucleolar RNA-associated protein 17,U3 snoRNA-associated protein 17 |
| 28 | DA (B1) | Periodic tryptophan protein 2 | polymer | 900 | 101467.4 | 1 | UniProt (P25635) Pfam (PF00400) Pfam (PF04003) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U three protein 1,U3 small nucleolar RNA-associated protein 1,U3 snoRNA-associated protein 1 |
| 29 | EA (B2) | U3 small nucleolar RNA-associated protein 12 | polymer | 943 | 106481.1 | 1 | UniProt (Q12220) Pfam (PF00400) Pfam (PF04003) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp12, U3 snoRNA-associated protein 12,DOM34-interacting protein 2,U three protein 12 |
| 30 | FA (B3) | U3 small nucleolar RNA-associated protein 13 | polymer | 817 | 91132.6 | 1 | UniProt (Q05946) Pfam (PF00400) Pfam (PF08625) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp13, U3 snoRNA-associated protein 13,U three protein 13 |
| 31 | GA (B8) | U3 small nucleolar RNA-associated protein 18 | polymer | 594 | 66494.3 | 1 | UniProt (P40362) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp18, U3 snoRNA-associated protein 18,U three protein 18 |
| 32 | HA (BE) | U3 small nucleolar RNA-associated protein 21 | polymer | 939 | 104927.8 | 1 | UniProt (Q06078) Pfam (PF00400) Pfam (PF04192) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp21, U3 snoRNA-associated protein 21,U three protein 21 |
| 33 | IA (B6) | U3 small nucleolar RNA-associated protein 6 | polymer | 440 | 52495.3 | 1 | UniProt (Q02354) Pfam (PF08640) Pfam (PF05843) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp6, U3 snoRNA-associated protein 6,U three protein 6 |
| 34 | JA (5C) | U3 small nucleolar RNA-associated protein 7 | polymer | 554 | 62418.6 | 1 | UniProt (P40055) Pfam (PF08149) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp7, U3 snoRNA-associated protein 7,U three protein 7 |
| 35 | KA (5D) | U3 small nucleolar RNA-associated protein 11 | polymer | 250 | 29806.3 | 1 | UniProt (P34247) Pfam (PF03998) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp11, U3 snoRNA-associated protein 11,U three protein 11 |
| 36 | LA (5E) | U3 small nucleolar RNA-associated protein MPP10 | polymer | 593 | 67042.5 | 1 | UniProt (P47083) Pfam (PF04006) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Mpp10, U3 snoRNA-associated protein MPP10,M phase phosphoprotein 10 |
| 37 | MA (5F) | U3 small nucleolar ribonucleoprotein protein IMP3 | polymer | 183 | 21928.5 | 1 | UniProt (P32899) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Imp3, U3 snoRNP protein IMP3,Interacting with MPP10 protein 3 |
| 38 | NA (5G) | U3 small nucleolar ribonucleoprotein protein IMP4 | polymer | 290 | 33536.2 | 1 | UniProt (P53941) Pfam (PF04427) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Imp4, U3 snoRNP protein IMP4,Interacting with MPP10 protein 4 |
| 39 | OA (5H) | Something about silencing protein 10 | polymer | 610 | 70364.4 | 1 | UniProt (Q12136) Pfam (PF04000) Pfam (PF09368) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sas10, U three protein 3,U3 small nucleolar RNA-associated protein 3,U3 snoRNA-associated protein 11 |
| 40 | PA (5I) | Protein SOF1 | polymer | 489 | 56888.9 | 1 | UniProt (P33750) Pfam (PF00400) Pfam (PF04158) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sof1, U3 small nucleolar RNA-associated protein SOF1,U3 snoRNA-associated protein SOF1 |
| 41 | QA (5J) | rRNA-processing protein FCF2 | polymer | 217 | 25689.2 | 1 | UniProt (Q12035) Pfam (PF08698) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | FAF1 copurifying factor 2 |
| 42 | RA (5K) | rRNA-processing protein FCF1 | polymer | 189 | 21649.7 | 1 | UniProt (Q05498) Pfam (PF04900) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | FAF1-copurifying factor 1 |
| 43 | SA (RD) | rRNA biogenesis protein RRP5 | polymer | 1729 | 193411.4 | 1 | UniProt (Q05022) Pfam (PF00575) Pfam (PF05843) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Ribosomal RNA-processing protein 5,U3 small nucleolar RNA-associated protein RRP5,U3 snoRNA-associated protein RRP5 |
| 44 | TA (RE) | U3 small nucleolar RNA-associated protein 22 | polymer | 1237 | 140660.1 | 1 | UniProt (P53254) Pfam (PF03813) Pfam (PF17403) Pfam (PF17404) Pfam (PF17405) Pfam (PF17406) Pfam (PF17407) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp22, U3 snoRNA-associated protein 22,U three protein 22 |
| 45 | UA (RF) | Ribosomal RNA-processing protein 7 | polymer | 297 | 34526.4 | 1 | UniProt (P25368) Pfam (PF17799) Pfam (PF12923) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rrp7 |
| 46 | VA (RJ) | Ribosome biogenesis protein BMS1 | polymer | 1183 | 135792.3 | 1 | UniProt (Q08965) Pfam (PF00004) Pfam (PF08142) Pfam (PF04950) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Bms1 |
| 47 | WA (RK) | RNA 3'-terminal phosphate cyclase-like protein | polymer | 367 | 40220.6 | 1 | UniProt (Q08096) Pfam (PF01137) Pfam (PF05189) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rcl1 |
| 48 | XA (RN) | Nucleolar complex protein 14 | polymer | 810 | 94463.2 | 1 | UniProt (Q99207) Pfam (PF04147) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nop14, U three protein 2,U3 small nucleolar RNA-associated protein 2,U3 snoRNA-associated protein 2 |
| 49 | YA (RP) | U3 small nucleolar RNA-associated protein 20 | polymer | 2493 | 287915.5 | 1 | UniProt (P35194) Pfam (PF07539) Pfam (PF20416) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 20,U three protein 20 |
| 50 | ZA (RQ) | U3 small nucleolar RNA-associated protein 14 | polymer | 899 | 103189.8 | 1 | UniProt (Q04500) Pfam (PF04615) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp14, U3 snoRNA-associated protein 14,U three protein 14 |
| 51 | AB (RT) | Pno1 | polymer | 326 | 36356.5 | 1 | Saccharomyces cerevisiae S288C (Baker's yeast) | ||
| 52 | BB (RZ) | Probable ATP-dependent RNA helicase DHR1 | polymer | 1267 | 145171.4 | 1 | UniProt (Q04217) Pfam (PF00270) Pfam (PF00271) Pfam (PF04408) Pfam (PF21010) Pfam (PF07717) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | DEAH box RNA helicase DHR1,Extracellular mutant protein 16 |
| 53 | CB (X1) | Unassigned peptides 1 | polymer | 300 | 25549.3 | 1 | Saccharomyces cerevisiae S288C (Baker's yeast) | ||
| 54 | DB, EB (Sc, 5K) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 55 | FB (RJ) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 56 | GB (RJ) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 57 | HB (RZ) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) |
Sequence modifications
5K: 1 - 189 (UniProt: Q05498)
| PDB | External Database | Details |
|---|---|---|
| Asn 138 | Asp 138 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 55 |
| Total formula weight | 4019396.4 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 1105.5 | |
| All* | Total formula weight | 4020501.9 |
