6ZQB
Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2
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 (UA) | Periodic tryptophan protein 2 | polymer | 923 | 104097.0 | 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 |
| 2 | B (UB) | Nucleolar complex protein 14 | polymer | 810 | 94463.2 | 1 | UniProt (Q99207) Pfam (PF04147) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U three protein 2,U3 small nucleolar RNA-associated protein 2,U3 snoRNA-associated protein 2 |
| 3 | C (UC) | 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) | U three protein 3,U3 small nucleolar RNA-associated protein 3,U3 snoRNA-associated protein 11 |
| 4 | D (UD) | U3 small nucleolar RNA-associated protein 4 | polymer | 776 | 87909.2 | 1 | UniProt (Q06679) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 4,U three protein 4,U3 protein 4 required for transcription,t-UTP4 |
| 5 | E (UE) | 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) | U3 snoRNA-associated protein 5,U three protein 5,U3 protein 5 required for transcription,t-UTP5 |
| 6 | F (UF) | 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) | U3 snoRNA-associated protein 6,U three protein 6 |
| 7 | G (UG) | U3 small nucleolar RNA-associated protein 7 | polymer | 554 | 62418.6 | 1 | UniProt (P40055) Pfam (PF00400) Pfam (PF08149) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 7,U three protein 7 |
| 8 | H (UH) | U3 small nucleolar RNA-associated protein 8 | polymer | 713 | 80269.6 | 1 | UniProt (P53276) Pfam (PF10395) Pfam (PF22542) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 8,U three protein 8,U3 protein 8 required for transcription,t-UTP8 |
| 9 | I (UI) | U3 small nucleolar RNA-associated protein 9 | polymer | 575 | 65347.3 | 1 | UniProt (P38882) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 9,U three protein 9,U3 protein 9 required for transcription,t-UTP9 |
| 10 | J (UJ) | 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) | U3 snoRNA-associated protein 10,U three protein 10,U3 protein 10 required for transcription,t-UTP10 |
| 11 | K (UK) | 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) | U3 snoRNA-associated protein 11,U three protein 11 |
| 12 | L (UL) | 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) | U3 snoRNA-associated protein 12,DOM34-interacting protein 2,U three protein 12 |
| 13 | M (UM) | 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) | U3 snoRNA-associated protein 13,U three protein 13 |
| 14 | N (UN) | U3 small nucleolar RNA-associated protein 14,U3 small nucleolar RNA-associated protein 14 | polymer | 145 | 17147.3 | 1 | UniProt (Q04500) Pfam (PF04615) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 14,U three protein 14,U3 snoRNA-associated protein 14,U three protein 14 |
| 15 | O (UO) | U3 small nucleolar RNA-associated protein 15 | polymer | 513 | 57765.3 | 1 | UniProt (Q04305) Pfam (PF00400) Pfam (PF09384) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein 15,U three protein 15,U3 protein 15 required for transcription,t-UTP15 |
| 16 | P (UP) | Bud site selection protein 21 | polymer | 214 | 24431.0 | 1 | UniProt (Q08492) Pfam (PF08297) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U three protein 16,U3 small nucleolar RNA-associated protein 16,U3 snoRNA-associated protein 16 |
| 17 | Q (UQ) | NET1-associated nuclear protein 1 | polymer | 896 | 101341.7 | 1 | UniProt (Q02931) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U three protein 17,t-17,U3 protein 17 required for transcription,U3 small nucleolar RNA-associated protein 17,U3 snoRNA-associated protein 17 |
| 18 | R (UR) | 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) | U3 snoRNA-associated protein 18,U three protein 18 |
| 19 | S (US) | Nucleolar complex protein 4 | polymer | 552 | 63707.8 | 1 | UniProt (Q06512) Pfam (PF03914) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U three protein 19,U3 small nucleolar RNA-associated protein 19,U3 snoRNA-associated protein 19 |
| 20 | T (UT) | 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 |
| 21 | U (UU) | 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) | U3 snoRNA-associated protein 21,U three protein 21 |
| 22 | V (UV) | 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) | U3 snoRNA-associated protein 22,U three protein 22 |
| 23 | W (UX) | rRNA-processing protein FCF1 | polymer | 189 | 21650.7 | 1 | UniProt (Q05498) Pfam (PF04900) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | FAF1-copurifying factor 1 |
| 24 | X (UZ) | Ribosome biogenesis protein UTP30 | polymer | 274 | 31668.9 | 1 | UniProt (P36144) Pfam (PF00687) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNP-associated protein UTP30 |
| 25 | Y, Z (CA, CB) | rRNA 2'-O-methyltransferase fibrillarin | polymer | 327 | 34525.4 | 2 | UniProt (P15646) Pfam (PF01269) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Histone-glutamine methyltransferase,U3 small nucleolar RNA-associated protein NOP1,U3 snoRNA-associated protein NOP1 |
| 26 | AA (CD) | Nucleolar protein 56 | polymer | 504 | 56961.2 | 1 | UniProt (Q12460) Pfam (PF08156) Pfam (PF01798) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Ribosome biosynthesis protein SIK1,Suppressor of I kappa b protein 1 |
| 27 | BA (CE) | 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 |
| 28 | CA, DA (CF, CG) | 13 kDa ribonucleoprotein-associated protein | polymer | 126 | 13582.9 | 2 | UniProt (P39990) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Small nuclear ribonucleoprotein-associated protein 1 |
| 29 | EA (CH) | Ribosomal RNA-processing protein 9 | polymer | 573 | 65147.0 | 1 | UniProt (Q06506) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 30 | FA (CI) | U3 small nucleolar ribonucleoprotein protein IMP3 | polymer | 183 | 21928.5 | 1 | UniProt (P32899) Pfam (PF01479) Pfam (PF00163) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNP protein IMP3,Interacting with MPP10 protein 3 |
| 31 | GA (CJ) | U3 small nucleolar ribonucleoprotein protein IMP4 | polymer | 290 | 33536.2 | 1 | UniProt (P53941) Pfam (PF04427) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNP protein IMP4,Interacting with MPP10 protein 4 |
| 32 | HA (CK) | 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) | U3 snoRNA-associated protein MPP10,M phase phosphoprotein 10 |
| 33 | IA (CL) | 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) | |
| 34 | JA (CM) | 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) | |
| 35 | KA (CN) | 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) | |
| 36 | LA, MA (JA, JB) | RNA cytidine acetyltransferase | polymer | 1056 | 119509.4 | 2 | UniProt (P53914) Pfam (PF08351) Pfam (PF05127) Pfam (PF13718) Pfam (PF13725) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | 18S rRNA cytosine acetyltransferase,Killer toxin-resistance protein 33,Ribosomal RNA cytidine acetyltransferase 1 |
| 37 | NA (JC) | Ribosome biogenesis protein ENP2 | polymer | 707 | 81864.2 | 1 | UniProt (P48234) Pfam (PF08159) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Essential nuclear protein 2 |
| 38 | OA (JE) | U3 small nucleolar ribonucleoprotein protein LCP5 | polymer | 357 | 40864.4 | 1 | UniProt (P40079) Pfam (PF04000) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 39 | PA, QA (JF, JG) | Ribosomal RNA small subunit methyltransferase NEP1 | polymer | 252 | 27936.5 | 2 | UniProt (Q06287) Pfam (PF03587) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | 18S rRNA (pseudouridine(1189)-N1)-methyltransferase,18S rRNA Psi1189 methyltransferase,Essential for mitotic growth protein 1,Nucleolar essential protein 1 |
| 40 | RA (JH) | Essential nuclear protein 1 | polymer | 483 | 55207.4 | 1 | UniProt (P38333) Pfam (PF05291) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 41 | SA (JJ) | Pre-rRNA-processing protein PNO1 | polymer | 274 | 30380.6 | 1 | UniProt (Q99216) Pfam (PF17903) Pfam (PF22891) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Partner of NOB1,Ribosomal RNA-processing protein 20 |
| 42 | TA (JK) | Protein BFR2 | polymer | 534 | 61285.0 | 1 | UniProt (Q06631) Pfam (PF13339) Pfam (PF08164) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Brefeldin A resistance protein 2 |
| 43 | UA (JM) | 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 |
| 44 | VA (JN) | Protein FAF1 | polymer | 346 | 38961.5 | 1 | UniProt (P40546) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Forty S assembly factor |
| 45 | WA (JO) | KRR1 small subunit processome component | polymer | 316 | 37226.3 | 1 | UniProt (P25586) Pfam (PF17903) Pfam (PF21800) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | KRR-R motif-containing protein 1,Ribosomal RNA assembly protein KRR1 |
| 46 | XA (JP) | Protein SOF1 | polymer | 489 | 56888.9 | 1 | UniProt (P33750) Pfam (PF00400) Pfam (PF04158) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 small nucleolar RNA-associated protein SOF1,U3 snoRNA-associated protein SOF1 |
| 47 | YA (JQ) | Regulator of rDNA transcription protein 14 | polymer | 206 | 23898.3 | 1 | UniProt (P40470) Pfam (PF17075) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 48 | ZA (DA) | 40S ribosomal protein S1-A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP10A,Small ribosomal subunit protein eS1-A |
| 49 | AB (DE) | 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,Small ribosomal subunit protein eS4-A,YS6 |
| 50 | BB (DF) | Rps5p | polymer | 225 | 25072.6 | 1 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 51 | CB (DG) | 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,Small ribosomal subunit protein eS6-A,YS4 |
| 52 | DB (DH) | 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,Small ribosomal subunit protein eS7-A |
| 53 | EB (DI) | 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,Small ribosomal subunit protein eS8-A,YS9 |
| 54 | FB (DJ) | 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,Small ribosomal subunit protein uS4-A,YP28,YS11 |
| 55 | GB (DL) | 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,Small ribosomal subunit protein uS17-A,YS12 |
| 56 | HB (DN) | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S27a,Small ribosomal subunit protein uS15,YS15 |
| 57 | IB (DO) | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP59A,Small ribosomal subunit protein uS11-A |
| 58 | JB (DQ) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61R,Small ribosomal subunit protein uS9-A |
| 59 | KB (DS) | 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18 | polymer | 147 | 16303.9 | 1 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Small ribosomal subunit protein uS13-A |
| 60 | LB (DW) | 40S ribosomal protein S22-A | polymer | 130 | 14650.1 | 1 | UniProt (P0C0W1) Pfam (PF00410) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22 |
| 61 | MB (DX) | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) Pfam (PF00164) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP37,S28,Small ribosomal subunit protein uS12-A,YS14 |
| 62 | NB (DY) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50,Small ribosomal subunit protein eS24-A |
| 63 | OB (Db) | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 64 | PB (Dc) | 40S ribosomal protein S28-A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S33,Small ribosomal subunit protein eS28-A,YS27 |
| 65 | QB (D2) | 5ETS RNA | polymer | 700 | 225543.1 | 1 | Saccharomyces cerevisiae S288C | ||
| 66 | RB (D3) | 18S rRNA | polymer | 1808 | 582381.7 | 1 | Saccharomyces cerevisiae S288C | ||
| 67 | SB (D4) | U3 snoRNA | polymer | 175 | 56132.2 | 1 | Saccharomyces cerevisiae S288C | ||
| 68 | TB, VB (UX, Db) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 69 | UB (CL) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) |
Sequence modifications
UN: 276 - 349 (UniProt: Q04500)
UN: 827 - 897 (UniProt: Q04500)
DS: 1 - 122 (UniProt: P0CX55)
DS: 123 - 147 (PDB: 6ZQB)
UN: 827 - 897 (UniProt: Q04500)
DS: 1 - 122 (UniProt: P0CX55)
DS: 123 - 147 (PDB: 6ZQB)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 71 |
| Total formula weight | 4575774.5 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 654.0 | |
| All* | Total formula weight | 4576428.5 |
