8CBJ
Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex
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 (b) | 40S ribosomal protein S27-A | polymer | 82 | 8893.4 | 1 | UniProt (P35997) Pfam (PF01667) | Saccharomyces cerevisiae W303 | RP61,Small ribosomal subunit protein eS27-A,YS20 |
| 2 | B (c) | 40S ribosomal protein S28-A | polymer | 67 | 7605.8 | 1 | UniProt (Q3E7X9) Pfam (PF01200) | Saccharomyces cerevisiae W303 | S33,Small ribosomal subunit protein eS28-A,YS27 |
| 3 | C (d) | RPS29A isoform 1 | polymer | 56 | 6675.7 | 1 | UniProt (P41057) Pfam (PF00253) | Saccharomyces cerevisiae W303 | |
| 4 | D (e) | 40S ribosomal protein S30-A | polymer | 63 | 7137.5 | 1 | UniProt (P0CX33) Pfam (PF04758) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein eS30-A |
| 5 | E (g) | Guanine nucleotide-binding protein subunit beta-like protein | polymer | 319 | 34841.2 | 1 | UniProt (P38011) Pfam (PF00400) | Saccharomyces cerevisiae W303 | Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1 |
| 6 | F (h) | Pre-rRNA-processing protein PNO1 | polymer | 274 | 30380.6 | 1 | UniProt (A0A8H4F7A6) Pfam (PF17903) Pfam (PF22891) UniProt (by SIFTS) (Q99216) | Saccharomyces cerevisiae W303 | |
| 7 | G (i) | ENP1 isoform 1 | polymer | 483 | 55207.4 | 1 | UniProt (A0A8H4BTD0) Pfam (PF05291) UniProt (by SIFTS) (P38333) | Saccharomyces cerevisiae W303 | |
| 8 | H (j) | LTV1 isoform 1 | polymer | 463 | 53463.3 | 1 | UniProt (A0A8H4F8Z0) Pfam (PF04180) UniProt (by SIFTS) (P34078) | Saccharomyces cerevisiae W303 | |
| 9 | I (k) | TSR1 isoform 1 | polymer | 788 | 90876.5 | 1 | UniProt (A0A8H8UMM1) Pfam (PF22298) Pfam (PF08142) Pfam (PF04950) UniProt (by SIFTS) (Q07381) | Saccharomyces cerevisiae W303 | |
| 10 | J (l) | non-specific serine/threonine protein kinase | polymer | 425 | 49192.9 | 1 | UniProt (A0A6A5Q8T7) Pfam (PF09202) Pfam (PF01163) UniProt (by SIFTS) (P40160) | Saccharomyces cerevisiae W303 | |
| 11 | K (A) | 40S ribosomal protein S0-A | polymer | 252 | 28083.4 | 1 | UniProt (B3LI22) Pfam (PF00318) UniProt (by SIFTS) (P32905) | Saccharomyces cerevisiae W303 | Nucleic acid-binding protein NAB1A |
| 12 | L (B) | 40S ribosomal protein S1-A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae W303 | RP10A,Small ribosomal subunit protein eS1-A |
| 13 | M (C) | 40S ribosomal protein S2 | polymer | 254 | 27490.8 | 1 | UniProt (P25443) Pfam (PF00333) Pfam (PF03719) | Saccharomyces cerevisiae W303 | Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5 |
| 14 | N (D) | 40S ribosomal protein S3 | polymer | 240 | 26542.8 | 1 | UniProt (P05750) Pfam (PF07650) Pfam (PF00189) | Saccharomyces cerevisiae W303 | RP13,Small ribosomal subunit protein uS3,YS3 |
| 15 | O (E) | 40S ribosomal protein S4-B | polymer | 261 | 29469.3 | 1 | UniProt (P0CX36) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) Pfam (PF08071) Pfam (PF01479) | Saccharomyces cerevisiae W303 | RP5,S7,Small ribosomal subunit protein eS4-B,YS6 |
| 16 | P (F) | 40S ribosomal protein S5 | polymer | 225 | 25072.6 | 1 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae W303 | RP14,S2,Small ribosomal subunit protein uS7,YS8 |
| 17 | Q (G) | 40S ribosomal protein S6-B | polymer | 236 | 27054.5 | 1 | UniProt (P0CX38) Pfam (PF01092) | Saccharomyces cerevisiae W303 | RP9,S10,Small ribosomal subunit protein eS6-B,YS4 |
| 18 | R (H) | 40S ribosomal protein S7-A | polymer | 190 | 21658.2 | 1 | UniProt (P26786) Pfam (PF01251) | Saccharomyces cerevisiae W303 | RP30,RP40,Small ribosomal subunit protein eS7-A |
| 19 | S (I) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 1 | UniProt (P0CX39) Pfam (PF01201) | Saccharomyces cerevisiae W303 | |
| 20 | T (J) | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae W303 | |
| 21 | U (L) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) | Saccharomyces cerevisiae W303 | |
| 22 | V (M) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae (baker's yeast) | Small ribosomal subunit protein eS12 |
| 23 | W (N) | 40S ribosomal protein S13 | polymer | 151 | 17059.9 | 1 | UniProt (P05756) Pfam (PF08069) Pfam (PF00312) | Saccharomyces cerevisiae W303 | S27a,Small ribosomal subunit protein uS15,YS15 |
| 24 | X (O) | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae W303 | |
| 25 | Y (P) | RPS15 isoform 1 | polymer | 142 | 16031.9 | 1 | UniProt (Q01855) Pfam (PF00203) | Saccharomyces cerevisiae W303 | |
| 26 | Z (Q) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae W303 | RP61R,Small ribosomal subunit protein uS9-A |
| 27 | AA (R) | 40S ribosomal protein S17-A | polymer | 136 | 15820.4 | 1 | UniProt (P02407) Pfam (PF00833) | Saccharomyces cerevisiae (baker's yeast) | RP51A,Small ribosomal subunit protein eS17-A |
| 28 | BA (S) | 40S ribosomal protein S18-A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein uS13-A |
| 29 | CA (T) | 40S ribosomal protein S19-A | polymer | 144 | 15942.1 | 1 | UniProt (P07280) Pfam (PF01090) | Saccharomyces cerevisiae W303 | RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A |
| 30 | DA (U) | 40S ribosomal protein S20 | polymer | 121 | 13929.0 | 1 | UniProt (P38701) Pfam (PF00338) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein uS10 |
| 31 | EA (V) | 40S ribosomal protein S21-A | polymer | 87 | 9758.8 | 1 | UniProt (P0C0V8) Pfam (PF01249) | Saccharomyces cerevisiae W303 | S26,Small ribosomal subunit protein eS21-A,YS25 |
| 32 | FA (W) | 40S ribosomal protein S22-A | polymer | 130 | 14650.1 | 1 | UniProt (P0C0W1) Pfam (PF00410) | Saccharomyces cerevisiae W303 | |
| 33 | GA (X) | 40S ribosomal protein S23-A | polymer | 145 | 16073.9 | 1 | UniProt (P0CX29) Pfam (PF00164) | Saccharomyces cerevisiae W303 | RP37,S28,Small ribosomal subunit protein uS12-A,YS14 |
| 34 | HA (Y) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae W303 | RP50,Small ribosomal subunit protein eS24-A |
| 35 | IA (Z) | 40S ribosomal protein S25-A | polymer | 108 | 12067.3 | 1 | UniProt (Q3E792) Pfam (PF03297) | Saccharomyces cerevisiae W303 | RP45,S31,Small ribosomal subunit protein eS25-A,YS23 |
| 36 | JA (a) | 20S-pre-rRNA D-site endonuclease NOB1 | polymer | 459 | 51824.9 | 1 | UniProt (A0A6A5Q3F3) Pfam (PF17146) Pfam (PF08772) UniProt (by SIFTS) (Q08444) | Saccharomyces cerevisiae W303 | |
| 37 | KA (y) | rRNA adenine N(6)-methyltransferase | polymer | 318 | 36003.8 | 1 | UniProt (A0A6A5Q6M3) Pfam (PF00398) UniProt (by SIFTS) (P41819) | Saccharomyces cerevisiae W303 | |
| 38 | LA (2) | 20S pre-ribosomal RNA | polymer | 2012 | 647990.4 | 1 | Saccharomyces cerevisiae | ||
| 39 | MA (K) | OTU domain-containing protein 2 | polymer | 307 | 36157.0 | 1 | UniProt (P38747) Pfam (PF02338) | Saccharomyces cerevisiae W303 | |
| 40 | NA, OA (b, d) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 41 | AB, AC, BB, BC, CB... (2) | MAGNESIUM ION | non-polymer | 24.3 | 46 | Chemie (MG) |
Sequence modifications
A: 1 - 252 (UniProt: B3LI22)
K: 1 - 307 (UniProt: P38747)
| PDB | External Database | Details |
|---|---|---|
| Phe 206 | Asp 206 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 178 | Cys 178 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 39 |
| Total formula weight | 1602929.1 | |
| Non-Polymers* | Number of molecules | 48 |
| Total formula weight | 1248.8 | |
| All* | Total formula weight | 1604177.9 |
