7D5S
Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2)
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 (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 2 | B (5A) | 5' ETS | polymer | 700 | 225543.1 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 3 | C (SA) | 18S rRNA | polymer | 1808 | 582381.7 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 4 | D (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 |
| 5 | E (SK) | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF01479) Pfam (PF00163) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP21,S13,YP28,YS11 |
| 6 | F (SN) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 7 | G (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 |
| 8 | H (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 |
| 9 | I (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 |
| 10 | J (ST) | 40S ribosomal protein S18-A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Rps18, Small ribosomal subunit protein uS13-A |
| 11 | K (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 |
| 12 | L (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 |
| 13 | M, N (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 |
| 14 | O (3D) | Nucleolar protein 56 | polymer | 504 | 56961.2 | 1 | UniProt (Q12460) Pfam (PF08156) Pfam (PF01798) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nop56, Ribosome biosynthesis protein SIK1,Suppressor of I kappa b protein 1 |
| 15 | P (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 |
| 16 | Q (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 |
| 17 | R, S (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 |
| 18 | T (A4) | 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) | Utp4, U3 snoRNA-associated protein 4,U three protein 4,U3 protein 4 required for transcription,t-UTP4 |
| 19 | U (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 |
| 20 | V (A8) | 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) | Utp8, U3 snoRNA-associated protein 8,U three protein 8,U3 protein 8 required for transcription,t-UTP8 |
| 21 | W (A9) | U3 small nucleolar RNA-associated protein 9 | polymer | 575 | 65347.3 | 1 | UniProt (P38882) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp9, U3 snoRNA-associated protein 9,U three protein 9,U3 protein 9 required for transcription,t-UTP9 |
| 22 | X (AE) | U3 small nucleolar RNA-associated protein 10 | polymer | 1769 | 200299.0 | 1 | UniProt (P42945) Pfam (PF12397) Pfam (PF23243) 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 |
| 23 | Y (AF) | 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) | Utp15, U3 snoRNA-associated protein 15,U three protein 15,U3 protein 15 required for transcription,t-UTP15 |
| 24 | Z (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 |
| 25 | AA (B1) | Periodic tryptophan protein 2 | polymer | 923 | 104097.0 | 1 | UniProt (P25635) Pfam (PF00400) Pfam (PF04003) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp1, U three protein 1,U3 small nucleolar RNA-associated protein 1,U3 snoRNA-associated protein 1 |
| 26 | BA (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 |
| 27 | CA (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 |
| 28 | DA (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 |
| 29 | EA (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 |
| 30 | FA (B6) | U3 small nucleolar RNA-associated protein 6 | polymer | 440 | 52495.3 | 1 | UniProt (Q02354) Pfam (PF08640) Pfam (PF23240) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp6, U3 snoRNA-associated protein 6,U three protein 6 |
| 31 | GA (5B) | Bud site selection protein 21 | polymer | 214 | 24431.0 | 1 | UniProt (Q08492) Pfam (PF08297) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Bud21, U three protein 16,U3 small nucleolar RNA-associated protein 16,U3 snoRNA-associated protein 16 |
| 32 | HA (5C) | 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) | Utp7, U3 snoRNA-associated protein 7,U three protein 7 |
| 33 | IA (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 |
| 34 | JA (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 |
| 35 | KA (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 |
| 36 | LA (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 |
| 37 | MA (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 |
| 38 | NA (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 |
| 39 | OA (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 |
| 40 | PA (5K) | rRNA-processing protein FCF1 | polymer | 189 | 21650.7 | 1 | UniProt (Q05498) Pfam (PF04900) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp24, FAF1-copurifying factor 1 |
| 41 | QA (RC) | 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 |
| 42 | RA (RD) | rRNA biogenesis protein RRP5 | polymer | 1729 | 193411.4 | 1 | UniProt (Q05022) Pfam (PF00575) Pfam (PF23240) | 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 |
| 43 | SA (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 |
| 44 | TA (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 |
| 45 | UA, VA (RG, RH) | Ribosomal RNA small subunit methyltransferase NEP1 | polymer | 252 | 27936.5 | 2 | UniProt (Q06287) Pfam (PF03587) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Emg1, 18S rRNA (pseudouridine(1189)-N1)-methyltransferase,18S rRNA Psi1189 methyltransferase,Essential for mitotic growth protein 1,Nucleolar essential protein 1 |
| 46 | WA (RI) | Ribosome biogenesis protein UTP30 | polymer | 274 | 31668.9 | 1 | UniProt (P36144) Pfam (PF00687) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Utp30, U3 snoRNP-associated protein UTP30 |
| 47 | XA (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 |
| 48 | YA (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 |
| 49 | ZA (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 |
| 50 | AB (RO) | Nucleolar complex protein 4 | polymer | 552 | 63707.8 | 1 | UniProt (Q06512) Pfam (PF03914) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Noc4, U three protein 19,U3 small nucleolar RNA-associated protein 19,U3 snoRNA-associated protein 19 |
| 51 | BB (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 |
| 52 | CB (RS) | Essential nuclear protein 1 | polymer | 483 | 55207.4 | 1 | UniProt (P38333) Pfam (PF05291) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Enp1 |
| 53 | DB (RT) | Pno1 | polymer | 326 | 36356.5 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 54 | EB (RW) | Regulator of rDNA transcription protein 14 | polymer | 206 | 23898.3 | 1 | UniProt (P40470) Pfam (PF17075) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 55 | FB (X1) | Unassigned peptides 1 | polymer | 347 | 29549.3 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 56 | GB (5K) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 57 | HB (RJ) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 58 | IB (RJ) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 58 |
| Total formula weight | 4021261.0 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 612.9 | |
| All* | Total formula weight | 4021873.9 |
