5WYJ
Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1)
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 RNA | polymer | 333 | 106503.3 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 2 | B, C (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) | Histone-glutamine methyltransferase,U3 small nucleolar RNA-associated protein NOP1,U3 snoRNA-associated protein NOP1 |
| 3 | D (3D) | 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 |
| 4 | E (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 |
| 5 | F (3F) | Ribosomal RNA-processing protein 9 | polymer | 573 | 65147.0 | 1 | UniProt (Q06506) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 6 | G, H (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) | Small nuclear ribonucleoprotein-associated protein 1 |
| 7 | I (5A) | 5ETS RNA | polymer | 700 | 225543.1 | 1 | GenBank (1262303) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 8 | J (AA) | Utp4 | polymer | 776 | 66059.2 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 9 | K (AB) | Utp5 | polymer | 643 | 54740.6 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 10 | L (AC) | Utp8 | polymer | 713 | 60697.8 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 11 | M (AD) | Utp9 | polymer | 575 | 48953.4 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 12 | N (AE) | U3 small nucleolar RNA-associated protein 10,Utp10 | polymer | 1769 | 173592.4 | 1 | UniProt (P42945) Pfam (PF12397) | 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 |
| 13 | O (AF) | Utp15 | polymer | 513 | 43676.9 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 14 | P (AG) | Utp17 | polymer | 896 | 76271.4 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 15 | Q (B1) | 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) | |
| 16 | R (BA) | 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 |
| 17 | S (BB) | 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 |
| 18 | T (BC) | 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 |
| 19 | U (BD) | 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 |
| 20 | V (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) | U3 snoRNA-associated protein 21,U three protein 21 |
| 21 | W (CA) | 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) | |
| 22 | X (CB) | 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 | Y, Z (E1, E2) | 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 |
| 24 | AA (E3) | Essential nuclear protein 1 | polymer | 483 | 55207.4 | 1 | UniProt (P38333) Pfam (PF05291) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 25 | BA (E4) | Enp2 | polymer | 707 | 60187.1 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 26 | CA (K1) | 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 |
| 27 | DA (MA) | 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) | U3 snoRNP protein IMP3,Interacting with MPP10 protein 3 |
| 28 | EA (MB) | 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 |
| 29 | FA (MC) | Mpp10,U3 small nucleolar RNA-associated protein MPP10 | polymer | 593 | 54937.0 | 1 | UniProt (P47083) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U3 snoRNA-associated protein MPP10,M phase phosphoprotein 10 |
| 30 | GA (P1) | 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 |
| 31 | HA (R1) | 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) | |
| 32 | IA (R2) | 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 |
| 33 | JA (S1) | Sof1 | polymer | 489 | 41634.3 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 34 | KA (SA) | 18S ribosomal RNA | polymer | 1812 | 583636.6 | 1 | GenBank (874346701) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 35 | LA (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 |
| 36 | MA (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 |
| 37 | NA (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 |
| 38 | OA (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 |
| 39 | PA (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 |
| 40 | QA (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 |
| 41 | RA (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 |
| 42 | SA (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 |
| 43 | TA (SN) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 44 | UA (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) | S27a,YS15 |
| 45 | VA (SP) | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP59A |
| 46 | WA (SR) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61R |
| 47 | XA (SX) | 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,YP58,YS22 |
| 48 | YA (SY) | 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,YS14 |
| 49 | ZA (SZ) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP50 |
| 50 | AB (Sc) | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RP61,YS20 |
| 51 | BB (Sd) | 40S ribosomal protein S28-A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | S33,YS27 |
| 52 | CB (Sf) | 40S ribosomal protein S30-A | polymer | 63 | 7137.5 | 1 | UniProt (P0CX33) Pfam (PF04758) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 53 | DB (Sg) | Ubiquitin-40S ribosomal protein S31 | polymer | 152 | 17254.2 | 1 | UniProt (P05759) Pfam (PF00240) Pfam (PF01599) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 54 | EB (U1) | Utp7 | polymer | 554 | 47166.2 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 55 | FB (U2) | Utp11 | polymer | 250 | 21294.2 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 56 | GB (U3) | Utp20 | polymer | 2493 | 212188.8 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 57 | HB (U4) | 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 |
| 58 | IB (U5) | 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 |
| 59 | JB (UA) | Helical domain protein | polymer | 1615 | 137462.4 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 60 | KB (UB) | Helical domain protein | polymer | 987 | 84015.7 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
| 61 | LB (UC) | Unassigned helices | polymer | 1033 | 87930.4 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Sequence modifications
AE: 1 - 808 (UniProt: P42945)
AE: 809 - 1769 (PDB: 5WYJ)
MC: 1 - 428 (PDB: 5WYJ)
MC: 429 - 593 (UniProt: P47083)
AE: 809 - 1769 (PDB: 5WYJ)
MC: 1 - 428 (PDB: 5WYJ)
MC: 429 - 593 (UniProt: P47083)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 64 |
| Total formula weight | 4111922.2 | |
| All* | Total formula weight | 4111922.2 |
