8BHF
Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4
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 | A1 | Ribosomal protein L15 | polymer | 203 | 24076.1 | 1 | UniProt (G1T0C1) Pfam (PF00827) In PDB | Oryctolagus cuniculus (rabbit) | |
| 2 | B1 | 60S ribosomal protein L13a | polymer | 199 | 23144.9 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 3 | C1 | 60S ribosomal protein L17 | polymer | 153 | 17758.7 | 1 | UniProt (G1SCJ6) Pfam (PF00237) In PDB | Oryctolagus cuniculus (rabbit) | |
| 4 | D1 | Ribosomal protein L18 | polymer | 187 | 21568.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 5 | E1 | Ribosomal protein L19 | polymer | 180 | 21613.0 | 1 | UniProt (G1TYL6) Pfam (PF01280) In PDB | Oryctolagus cuniculus (rabbit) | |
| 6 | F1 | 60S ribosomal protein L18a | polymer | 176 | 20827.6 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 7 | G1 | 60S ribosomal protein L21 | polymer | 159 | 18478.8 | 1 | UniProt (G1SHQ2) Pfam (PF01157) In PDB | Oryctolagus cuniculus (rabbit) | |
| 8 | H1 | 60S ribosomal protein L22 | polymer | 99 | 11495.3 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 9 | I1 | 60S ribosomal protein L23 | polymer | 139 | 14761.3 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 10 | J1 | TRASH domain-containing protein | polymer | 106 | 12267.3 | 1 | Oryctolagus cuniculus | ||
| 11 | K1 | Ribosomal protein L23/L25 N-terminal domain-containing protein | polymer | 118 | 13727.2 | 1 | UniProt (G1SE76) Pfam (PF03939) Pfam (PF00276) In PDB | Oryctolagus cuniculus (rabbit) | |
| 12 | L1 | Ribosomal protein L26 | polymer | 134 | 15891.8 | 1 | UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467) In PDB | Oryctolagus cuniculus (rabbit) | |
| 13 | M1 | 60S ribosomal protein L27 | polymer | 135 | 15704.6 | 1 | UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777) In PDB | Oryctolagus cuniculus (rabbit) | |
| 14 | N1 | 60S ribosomal protein L27a | polymer | 147 | 16489.4 | 1 | UniProt (G1SNY0) Pfam (PF00828) In PDB | Oryctolagus cuniculus (rabbit) | |
| 15 | O1 | 60S ribosomal protein L29 | polymer | 116 | 13401.0 | 1 | UniProt (G1SGR6) Pfam (PF01779) In PDB | Oryctolagus cuniculus (rabbit) | |
| 16 | P1 | 60S ribosomal protein L30 | polymer | 98 | 10914.8 | 1 | UniProt (G1TDL2) Pfam (PF01248) In PDB | Oryctolagus cuniculus (rabbit) | |
| 17 | Q1 | 60S ribosomal protein L31 | polymer | 107 | 12635.7 | 1 | UniProt (G1SHG0) Pfam (PF01198) In PDB | Oryctolagus cuniculus (rabbit) | |
| 18 | R1 | Ribosomal protein L32 | polymer | 128 | 15022.0 | 1 | UniProt (G1U437) Pfam (PF01655) UniProt (by SIFTS) (G1TUN8) In PDB | Oryctolagus cuniculus (rabbit) | |
| 19 | S1 | 60S ribosomal protein L35a | polymer | 109 | 12449.6 | 1 | UniProt (G1SF08) Pfam (PF01247) In PDB | Oryctolagus cuniculus (rabbit) | |
| 20 | T1 | 60S ribosomal protein L34 | polymer | 114 | 12994.6 | 1 | UniProt (G1TXG5) Pfam (PF01199) In PDB | Oryctolagus cuniculus (rabbit) | |
| 21 | U1 | 60S ribosomal protein L35 | polymer | 122 | 14435.4 | 1 | UniProt (G1SIT5) Pfam (PF00831) In PDB | Oryctolagus cuniculus (rabbit) | |
| 22 | V1 | 60S ribosomal protein L36 | polymer | 102 | 11888.4 | 1 | UniProt (G1TBH2) Pfam (PF01158) In PDB | Oryctolagus cuniculus (rabbit) | |
| 23 | W1 | Ribosomal protein L37 | polymer | 86 | 10090.9 | 1 | UniProt (U3KPD5) Pfam (PF01907) In PDB | Oryctolagus cuniculus (rabbit) | |
| 24 | X1 | 60S ribosomal protein L38 | polymer | 69 | 8107.8 | 1 | UniProt (G1U001) Pfam (PF01781) In PDB | Oryctolagus cuniculus (rabbit) | |
| 25 | Y1 | 60S ribosomal protein L39-like | polymer | 50 | 6324.6 | 1 | UniProt (G1TTN1) Pfam (PF00832) In PDB | Oryctolagus cuniculus (rabbit) | |
| 26 | Z1 | Ubiquitin-60S ribosomal protein L40 | polymer | 52 | 6199.6 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 27 | a1 | 60S ribosomal protein L41 | polymer | 25 | 3473.5 | 1 | UniProt (A0A087WNH4) Pfam (PF05162) In PDB | Oryctolagus cuniculus (rabbit) | |
| 28 | b1 | Ribosomal protein L36a like | polymer | 104 | 12198.6 | 1 | UniProt (G1T040) Pfam (PF00935) In PDB | Oryctolagus cuniculus (rabbit) | |
| 29 | c1 | 60S ribosomal protein L37a | polymer | 91 | 10168.2 | 1 | UniProt (G1SY53) Pfam (PF01780) In PDB | Oryctolagus cuniculus (rabbit) | |
| 30 | d1 | 60S ribosomal protein L28 | polymer | 124 | 14220.7 | 1 | UniProt (G1U7L1) Pfam (PF01778) In PDB | Oryctolagus cuniculus (rabbit) | |
| 31 | e1 | 60S acidic ribosomal protein P0 | polymer | 196 | 21521.1 | 1 | UniProt (G1SPK4) Pfam (PF00466) Pfam (PF17777) In PDB | Oryctolagus cuniculus (rabbit) | |
| 32 | f1 | 60S ribosomal protein L12 | polymer | 153 | 16561.1 | 1 | UniProt (G1SMR7) Pfam (PF03946) Pfam (PF00298) In PDB | Oryctolagus cuniculus (rabbit) | |
| 33 | l1 | 60S ribosomal protein L10a | polymer | 206 | 23599.9 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 34 | m1 | mRNA | polymer | 3 | 896.6 | 1 | Oryctolagus cuniculus | ||
| 35 | n1 | CCR4-NOT transcription complex subunit 3 | polymer | 236 | 28090.8 | 1 | UniProt (B7Z6J7) Pfam (PF04065) In PDB | Homo sapiens (human) | cDNA FLJ61662,highly similar to CCR4-NOT transcription complex subunit 3 |
| 36 | 21 | P-site tRNA | polymer | 76 | 24456.5 | 1 | Oryctolagus cuniculus | ||
| 37 | 11 | nascent chain | polymer | 5 | 501.6 | 1 | Oryctolagus cuniculus | ||
| 38 | A2 | 28S ribosomal RNA | polymer | 5051 | 1634382.1 | 1 | Oryctolagus cuniculus | ||
| 39 | B2 | 5S ribosomal RNA | polymer | 119 | 38385.8 | 1 | GenBank (4CXE_4) | Oryctolagus cuniculus (rabbit) | |
| 40 | C2 | 5.8S ribosomal RNA | polymer | 156 | 50143.6 | 1 | GenBank (4CXE_3) | Oryctolagus cuniculus (rabbit) | |
| 41 | A3 | 18S ribosomal RNA | polymer | 1697 | 547733.1 | 1 | Oryctolagus cuniculus | ||
| 42 | B3 | 40S_SA_C domain-containing protein | polymer | 217 | 24361.9 | 1 | UniProt (G1TJH8) Pfam (PF00318) In PDB | Oryctolagus cuniculus (rabbit) | |
| 43 | C3 | 40S ribosomal protein S3a | polymer | 213 | 24759.1 | 1 | UniProt (G1SS70) Pfam (PF01015) In PDB | Oryctolagus cuniculus (rabbit) | |
| 44 | D3 | 40S ribosomal protein S2 | polymer | 221 | 24441.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 45 | E3 | Ribosomal protein S3 | polymer | 228 | 25215.6 | 1 | UniProt (G1TNM3) Pfam (PF07650) Pfam (PF00189) In PDB | Oryctolagus cuniculus (rabbit) | |
| 46 | F3 | 40S ribosomal protein S4 | polymer | 262 | 29523.7 | 1 | UniProt (G1TK17) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) Pfam (PF08071) In PDB | Oryctolagus cuniculus (rabbit) | |
| 47 | G3 | Ribosomal protein S5 | polymer | 191 | 21525.9 | 1 | UniProt (G1TFM5) Pfam (PF00177) In PDB | Oryctolagus cuniculus (rabbit) | |
| 48 | H3 | 40S ribosomal protein S6 | polymer | 237 | 27471.5 | 1 | UniProt (G1TM55) Pfam (PF01092) In PDB | Oryctolagus cuniculus (rabbit) | |
| 49 | I3 | 40S ribosomal protein S7 | polymer | 189 | 21629.3 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 50 | J3 | 40S ribosomal protein S8 | polymer | 206 | 24003.0 | 1 | UniProt (G1TJW1) Pfam (PF01201) In PDB | Oryctolagus cuniculus (rabbit) | |
| 51 | K3 | Ribosomal protein S9 (Predicted) | polymer | 185 | 21649.6 | 1 | UniProt (B7NZS8) Pfam (PF00163) Pfam (PF01479) In PDB | Oryctolagus cuniculus (rabbit) | |
| 52 | L3 | Plectin/S10 N-terminal domain-containing protein | polymer | 96 | 11529.7 | 1 | UniProt (G1TPV3) Pfam (PF03501) In PDB | Oryctolagus cuniculus (rabbit) | |
| 53 | M3 | 40S ribosomal protein S11 | polymer | 151 | 17586.8 | 1 | UniProt (G1TRM4) Pfam (PF16205) Pfam (PF00366) In PDB | Oryctolagus cuniculus (rabbit) | |
| 54 | N3 | 40S ribosomal protein S12 | polymer | 117 | 13048.2 | 1 | UniProt (G1SFR8) Pfam (PF01248) In PDB | Oryctolagus cuniculus (rabbit) | |
| 55 | O3 | ribosomal protein uS15 | polymer | 149 | 17057.1 | 1 | UniProt (G1SP51) Pfam (PF08069) Pfam (PF00312) In PDB | Oryctolagus cuniculus (rabbit) | |
| 56 | P3 | Ribosomal protein S14 | polymer | 136 | 14544.7 | 1 | UniProt (G1T1F0) Pfam (PF00411) In PDB | Oryctolagus cuniculus (rabbit) | |
| 57 | Q3 | 40S ribosomal protein S15 | polymer | 129 | 15115.8 | 1 | UniProt (G1U0Q2) Pfam (PF00203) In PDB | Oryctolagus cuniculus (rabbit) | |
| 58 | R3 | Ribosomal protein S16 | polymer | 142 | 16032.8 | 1 | UniProt (G1SGX4) Pfam (PF00380) In PDB | Oryctolagus cuniculus (rabbit) | |
| 59 | S3 | 40S ribosomal protein S17 | polymer | 132 | 15250.7 | 1 | UniProt (G1TU13) Pfam (PF00833) In PDB | Oryctolagus cuniculus (rabbit) | |
| 60 | T3 | 40S ribosomal protein S18 | polymer | 144 | 16898.6 | 1 | UniProt (G1SZI5) Pfam (PF00416) UniProt (by SIFTS) (G1TPG3) In PDB | Oryctolagus cuniculus (rabbit) | |
| 61 | U3 | 40S ribosomal protein S19 | polymer | 141 | 15611.0 | 1 | UniProt (G1TN62) Pfam (PF01090) In PDB | Oryctolagus cuniculus (rabbit) | |
| 62 | V3 | Ribosomal protein S20 | polymer | 100 | 11395.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 63 | W3 | 40S ribosomal protein S21 | polymer | 83 | 9124.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 64 | X3 | Ribosomal protein S15a | polymer | 129 | 14734.4 | 1 | UniProt (G1TG89) Pfam (PF00410) In PDB | Oryctolagus cuniculus (rabbit) | |
| 65 | Y3 | Ribosomal protein S23 | polymer | 141 | 15626.4 | 1 | UniProt (G1SZ47) Pfam (PF00164) In PDB | Oryctolagus cuniculus (rabbit) | |
| 66 | Z3 | 40S ribosomal protein S24 | polymer | 124 | 14432.1 | 1 | UniProt (G1T3D8) Pfam (PF01282) In PDB | Oryctolagus cuniculus (rabbit) | |
| 67 | a3 | 40S ribosomal protein S25 | polymer | 75 | 8526.1 | 1 | UniProt (G1TDB3) Pfam (PF03297) In PDB | Oryctolagus cuniculus (rabbit) | |
| 68 | b3 | 40S ribosomal protein S26 | polymer | 101 | 11645.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 69 | c3 | 40S ribosomal protein S27 | polymer | 83 | 9349.0 | 1 | UniProt (G1TZ76) Pfam (PF01667) In PDB | Oryctolagus cuniculus (rabbit) | |
| 70 | d3 | Ribosomal protein S28 | polymer | 62 | 7007.1 | 1 | UniProt (G1TIB4) Pfam (PF01200) In PDB | Oryctolagus cuniculus (rabbit) | |
| 71 | e3 | 40S ribosomal protein S29 | polymer | 55 | 6559.6 | 1 | UniProt (G1U7M4) Pfam (PF00253) In PDB | Oryctolagus cuniculus (rabbit) | |
| 72 | f3 | Ubiquitin-like domain-containing protein | polymer | 57 | 6512.7 | 1 | UniProt (A0A5F9D9G5) Pfam (PF04758) In PDB | Oryctolagus cuniculus (rabbit) | |
| 73 | g3 | Ubiquitin-40S ribosomal protein S27a | polymer | 68 | 7986.4 | 1 | UniProt (G1SK22) Pfam (PF00240) Pfam (PF01599) In PDB | Oryctolagus cuniculus (rabbit) | |
| 74 | h3 | Ribosomal protein RACK1 | polymer | 313 | 34669.1 | 1 | UniProt (G1SJB4) Pfam (PF00400) In PDB | Oryctolagus cuniculus (rabbit) | |
| 75 | j3 | 60S ribosomal protein L8 | polymer | 248 | 26998.6 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 76 | k3 | Ribosomal protein L3 | polymer | 394 | 45119.8 | 1 | UniProt (G1TL06) Pfam (PF00297) In PDB | Oryctolagus cuniculus (rabbit) | |
| 77 | l3 | 60S ribosomal protein L4 | polymer | 362 | 41101.4 | 1 | UniProt (G1SVW5) Pfam (PF00573) Pfam (PF14374) In PDB | Oryctolagus cuniculus (rabbit) | |
| 78 | m3 | 60S ribosomal protein L5 | polymer | 293 | 34077.4 | 1 | UniProt (G1SYJ6) UniProt (by SIFTS) (P19949) In PDB | Oryctolagus cuniculus (rabbit) | |
| 79 | n3 | 60S ribosomal protein L6 | polymer | 251 | 28818.3 | 1 | UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159) In PDB | Oryctolagus cuniculus (rabbit) | |
| 80 | o3 | 60S ribosomal protein L7 | polymer | 225 | 26658.8 | 1 | UniProt (G1SV32) Pfam (PF08079) Pfam (PF00327) In PDB | Oryctolagus cuniculus (rabbit) | |
| 81 | p3 | 60S ribosomal protein L7a | polymer | 240 | 27351.4 | 1 | UniProt (G1STW0) Pfam (PF01248) In PDB | Oryctolagus cuniculus (rabbit) | |
| 82 | q3 | 60S ribosomal protein L9 | polymer | 190 | 21627.2 | 1 | UniProt (G1SWI6) Pfam (PF00347) In PDB | Oryctolagus cuniculus (rabbit) | |
| 83 | r3 | Ribosomal protein L10 | polymer | 213 | 24511.9 | 1 | UniProt (B7NZQ2) Pfam (PF00252) In PDB | Oryctolagus cuniculus (rabbit) | Ribosomal protein L10 (Predicted) |
| 84 | s3 | 60S ribosomal protein L11 | polymer | 170 | 19399.5 | 1 | UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673) In PDB | Oryctolagus cuniculus (rabbit) | |
| 85 | t3 | 60S ribosomal protein L13 | polymer | 210 | 24200.5 | 1 | UniProt (G1TKB3) Pfam (PF01294) In PDB | Oryctolagus cuniculus (rabbit) | |
| 86 | u3 | 60S ribosomal protein L14 | polymer | 138 | 16217.4 | 1 | UniProt (G1SZ12) Pfam (PF01929) In PDB | Oryctolagus cuniculus (rabbit) | |
| 87 | A2, B2, A3, j3, r3... | MAGNESIUM ION | non-polymer | 24.3 | 275 | Chemie (MG) | |||
| 88 | b3, e3, T1, W1, Z1... | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) |
Sequence modifications
E1: 2 - 181 (UniProt: G1TYL6)
V1: 2 - 103 (UniProt: G1TBH2)
X1: 2 - 70 (UniProt: G1U001)
F3: 2 - 263 (UniProt: G1TK17)
J3: 2 - 207 (UniProt: G1TJW1)
U3: 3 - 143 (UniProt: G1TN62)
p3: 80 - 319 (UniProt: G1STW0)
t3: 2 - 211 (UniProt: G1TKB3)
| PDB | External Database | Details |
|---|---|---|
| Arg 38 | His 38 | conflict |
| Arg 151 | His 151 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 31 | Arg 31 | conflict |
| Met 58 | Ile 58 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Lys 24 | Asn 24 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 25 | Ser 25 | conflict |
| Arg 51 | Lys 51 | conflict |
| Thr 78 | Ala 78 | conflict |
| Val 156 | Met 156 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 47 | Gly 47 | variant |
| PDB | External Database | Details |
|---|---|---|
| Gly 119 | Trp 119 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 244 | Cys 244 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 74 | His 74 | conflict |
| Arg 190 | His 190 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 86 |
| Total formula weight | 3699509.5 | |
| Non-Polymers* | Number of molecules | 282 |
| Total formula weight | 7141.7 | |
| All* | Total formula weight | 3706651.2 |
