8CAH
Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (l) | Eukaryotic translation initiation factor 3 subunit I | polymer | 347 | 38803.4 | 1 | UniProt (A0A6A5PTA5) Pfam (PF00400) UniProt (by SIFTS) (P40217) | Saccharomyces cerevisiae W303 | |
| 2 | B (r) | Eukaryotic translation initiation factor 3 subunit G | polymer | 274 | 30547.5 | 1 | UniProt (A0A8H8UNW9) Pfam (PF12353) Pfam (PF00076) UniProt (by SIFTS) (Q04067) | Saccharomyces cerevisiae W303 | |
| 3 | C (o) | Eukaryotic translation initiation factor 3 subunit A | polymer | 964 | 110517.6 | 1 | UniProt (P38249) Pfam (PF22591) | Saccharomyces cerevisiae W303 | eIF3a,Eukaryotic translation initiation factor 3 110 kDa subunit homolog,eIF3 p110,Translation initiation factor eIF3,p110 subunit homolog |
| 4 | D (p) | Eukaryotic translation initiation factor 3 subunit B | polymer | 763 | 88241.8 | 1 | UniProt (A0A8H4F8W9) Pfam (PF00076) Pfam (PF08662) UniProt (by SIFTS) (P06103) | Saccharomyces cerevisiae W303 | |
| 5 | E (q) | Eukaryotic translation initiation factor 3 subunit C | polymer | 812 | 93310.2 | 1 | UniProt (A0A8H4BZ29) Pfam (PF05470) Pfam (PF01399) UniProt (by SIFTS) (P32497) | Saccharomyces cerevisiae W303 | |
| 6 | F (i) | Eukaryotic translation initiation factor 4C | polymer | 153 | 17462.2 | 1 | UniProt (A0A6A5PU90) Pfam (PF01176) UniProt (by SIFTS) (P38912) | Saccharomyces cerevisiae W303 | |
| 7 | G (m) | SUI1 isoform 1 | polymer | 108 | 12330.1 | 1 | UniProt (A0A6A5Q4K5) Pfam (PF01253) UniProt (by SIFTS) (P32911) | Saccharomyces cerevisiae W303 | |
| 8 | H (j) | RNA recognition motif (unknown) | polymer | 77 | 6571.1 | 1 | Saccharomyces cerevisiae W303 | ||
| 9 | I (2) | 18S ribosomal RNA | polymer | 1800 | 579761.9 | 1 | Saccharomyces cerevisiae W303 | ||
| 10 | J (P) | 40S ribosomal protein S0-A | polymer | 252 | 28051.3 | 1 | UniProt (P32905) Pfam (PF00318) | Saccharomyces cerevisiae W303 | Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A |
| 11 | K (Q) | 40S ribosomal protein S1-A | polymer | 255 | 28798.5 | 1 | UniProt (P33442) Pfam (PF01015) | Saccharomyces cerevisiae W303 | RP10A,Small ribosomal subunit protein eS1-A |
| 12 | L (R) | 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 |
| 13 | M (S) | 40S ribosomal protein S4-B | polymer | 261 | 29469.3 | 1 | UniProt (P0CX36) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) | Saccharomyces cerevisiae W303 | RP5,S7,Small ribosomal subunit protein eS4-B,YS6 |
| 14 | N (T) | 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 |
| 15 | O (V) | 40S ribosomal protein S8-A | polymer | 200 | 22537.8 | 1 | UniProt (P0CX39) Pfam (PF01201) | Saccharomyces cerevisiae W303 | |
| 16 | P (W) | 40S ribosomal protein S9-A | polymer | 197 | 22487.9 | 1 | UniProt (O13516) Pfam (PF00163) Pfam (PF01479) | Saccharomyces cerevisiae W303 | |
| 17 | Q (X) | 40S ribosomal protein S11-A | polymer | 156 | 17785.9 | 1 | UniProt (P0CX47) Pfam (PF16205) Pfam (PF00366) | Saccharomyces cerevisiae W303 | |
| 18 | R (Y) | 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 |
| 19 | S (Z) | 40S ribosomal protein S14-A | polymer | 137 | 14562.7 | 1 | UniProt (P06367) Pfam (PF00411) | Saccharomyces cerevisiae W303 | |
| 20 | T (a) | 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 |
| 21 | U (b) | 40S ribosomal protein S22-A | polymer | 130 | 14650.1 | 1 | UniProt (P0C0W1) Pfam (PF00410) | Saccharomyces cerevisiae W303 | |
| 22 | V (c) | 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 |
| 23 | W (d) | 40S ribosomal protein S24-A | polymer | 135 | 15362.8 | 1 | UniProt (P0CX31) Pfam (PF01282) | Saccharomyces cerevisiae W303 | RP50,Small ribosomal subunit protein eS24-A |
| 24 | X (e) | 40S ribosomal protein S26-A | polymer | 119 | 13538.9 | 1 | UniProt (P39938) Pfam (PF01283) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein eS26-A |
| 25 | Y (f) | 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 |
| 26 | Z (g) | 40S ribosomal protein S30-A | polymer | 63 | 7137.5 | 1 | UniProt (P0CX33) Pfam (PF04758) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein eS30-A |
| 27 | AA (E) | RPS15 isoform 1 | polymer | 142 | 16031.9 | 1 | UniProt (Q01855) Pfam (PF00203) | Saccharomyces cerevisiae W303 | |
| 28 | BA (A) | 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 |
| 29 | CA (B) | 40S ribosomal protein S5 | polymer | 225 | 25072.6 | 1 | UniProt (P26783) Pfam (PF00177) | Saccharomyces cerevisiae W303 | RP14,S2,Small ribosomal subunit protein uS7,YS8 |
| 30 | DA (C) | 40S ribosomal protein S10-A | polymer | 105 | 12757.4 | 1 | UniProt (Q08745) Pfam (PF03501) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein eS10-A |
| 31 | EA (D) | 40S ribosomal protein S12 | polymer | 143 | 15488.6 | 1 | UniProt (P48589) Pfam (PF01248) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein eS12 |
| 32 | FA (F) | 40S ribosomal protein S16-A | polymer | 143 | 15877.5 | 1 | UniProt (P0CX51) Pfam (PF00380) | Saccharomyces cerevisiae W303 | RP61R,Small ribosomal subunit protein uS9-A |
| 33 | GA (H) | 40S ribosomal protein S17-A | polymer | 136 | 15820.4 | 1 | UniProt (P02407) Pfam (PF00833) | Saccharomyces cerevisiae W303 | RP51A,Small ribosomal subunit protein eS17-A |
| 34 | HA (I) | 40S ribosomal protein S18-A | polymer | 146 | 17071.6 | 1 | UniProt (P0CX55) Pfam (PF00416) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein uS13-A |
| 35 | IA (J) | 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 |
| 36 | JA (K) | 40S ribosomal protein S20 | polymer | 121 | 13929.0 | 1 | UniProt (P38701) Pfam (PF00338) | Saccharomyces cerevisiae W303 | Small ribosomal subunit protein uS10 |
| 37 | KA (L) | 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 |
| 38 | LA (M) | RPS29A isoform 1 | polymer | 56 | 6675.7 | 1 | UniProt (P41057) Pfam (PF00253) | Saccharomyces cerevisiae W303 | |
| 39 | MA (N) | 40S ribosomal protein S31 | polymer | 76 | 8703.5 | 1 | UniProt (P05759) Pfam (PF01599) | Saccharomyces cerevisiae W303 | CEP76,S37,Small ribosomal subunit protein eS31,YS24 |
| 40 | NA (O) | 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 |
| 41 | OA (h) | 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 |
| 42 | PA, QA (z, y) | Eukaryotic translation initiation factor 3 subunit J | polymer | 265 | 29611.2 | 2 | UniProt (A0A6A5PQW9) Pfam (PF08597) UniProt (by SIFTS) (Q05775) | Saccharomyces cerevisiae W303 | |
| 43 | RA (x) | RLI1 isoform 1 | polymer | 608 | 68433.2 | 1 | UniProt (A0A6A5Q259) Pfam (PF04068) Pfam (PF00037) Pfam (PF00005) UniProt (by SIFTS) (Q03195) | Saccharomyces cerevisiae W303 | |
| 44 | SA (k) | 60S ribosomal protein L40-A | polymer | 76 | 8576.8 | 1 | UniProt (P0CH08) Pfam (PF00240) | Saccharomyces cerevisiae W303 | CEP52,Large ribosomal subunit protein eL40-A |
| 45 | TA (n) | 60S ribosomal protein L41-A | polymer | 25 | 3354.2 | 1 | UniProt (P0CX86) Pfam (PF05162) | Saccharomyces cerevisiae W303 | L47,Large ribosomal subunit protein eL41-A,YL41 |
| 46 | UA (G) | OTU domain-containing protein 2 | polymer | 307 | 36157.0 | 1 | UniProt (P38747) Pfam (PF02338) | Saccharomyces cerevisiae W303 | |
| 47 | VA (U) | 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 |
| 48 | AB, AC, AD, BB, BC... (2, x, S, B) | MAGNESIUM ION | non-polymer | 24.3 | 80 | Chemie (MG) | |||
| 49 | XD, YD (M, N) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 50 | AE, ZD (x) | IRON/SULFUR CLUSTER | non-polymer | 351.6 | 2 | Chemie (SF4) | |||
| 51 | BE (x) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) |
Sequence modifications
k: 1 - 76 (UniProt: P0CH08)
G: 1 - 307 (UniProt: P38747)
| PDB | External Database | Details |
|---|---|---|
| Pro 19 | Ser 19 | conflict |
| Glu 24 | Asp 24 | conflict |
| Ala 28 | Ser 28 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 178 | Cys 178 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 48 |
| Total formula weight | 1740089.6 | |
| Non-Polymers* | Number of molecules | 85 |
| Total formula weight | 3205.7 | |
| All* | Total formula weight | 1743295.3 |
