8RJB
Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4
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 | 1 | Protein transport protein Sec61 subunit alpha isoform 1 | polymer | 476 | 52279.4 | 1 | UniProt (P38377) Pfam (PF10559) Pfam (PF00344) In PDB | Canis lupus familiaris (dog) | Sec61 alpha-1 |
2 | 2 | Protein transport protein Sec61 subunit beta | polymer | 96 | 9987.5 | 1 | UniProt (P60467) Pfam (PF03911) In PDB | Canis lupus familiaris (dog) | |
3 | 3 | Protein transport protein Sec61 subunit gamma | polymer | 68 | 7752.3 | 1 | UniProt (P60058) Pfam (PF00584) In PDB | Canis lupus familiaris (dog) | |
4 | 4 | Stress-associated endoplasmic reticulum protein | polymer | 66 | 7384.8 | 1 | UniProt (A0A8C0RGL8) Pfam (PF06624) In PDB | Canis lupus familiaris (dog) | |
5 | A | Ribosomal protein L8 | polymer | 257 | 28088.9 | 1 | UniProt (G1TT27) Pfam (PF00181) Pfam (PF03947) In PDB | Oryctolagus cuniculus (rabbit) | |
6 | B | Nascent chain | polymer | 229 | 23488.7 | 1 | Bos taurus | ||
7 | C | Large ribosomal subunit protein uL4 | polymer | 425 | 47727.6 | 1 | UniProt (A0A5F9C3C5) Pfam (PF00573) Pfam (PF14374) In PDB | Oryctolagus cuniculus (rabbit) | 60S ribosomal protein L4 |
8 | D | Ribosomal_L18_c domain-containing protein | polymer | 297 | 34481.8 | 1 | UniProt (G1SYJ6) UniProt (by SIFTS) (P19949) In PDB | Oryctolagus cuniculus (rabbit) | 60S ribosomal protein L5 |
9 | E | 60S ribosomal protein L6 | polymer | 291 | 33028.3 | 1 | UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159) In PDB | Oryctolagus cuniculus (rabbit) | |
10 | F | Ribosomal Protein uL30 | polymer | 247 | 29201.8 | 1 | UniProt (G1TUB1) Pfam (PF08079) Pfam (PF00327) In PDB | Oryctolagus cuniculus (rabbit) | |
11 | G | 60S ribosomal protein L7a | polymer | 319 | 36221.5 | 1 | UniProt (G1STW0) Pfam (PF01248) In PDB | Oryctolagus cuniculus (rabbit) | |
12 | H | 60S ribosomal protein L9 | polymer | 192 | 21871.4 | 1 | UniProt (G1SWI6) Pfam (PF00347) In PDB | Oryctolagus cuniculus (rabbit) | |
13 | I | 60S ribosomal protein L10 | polymer | 214 | 24643.1 | 1 | UniProt (B7NZQ2) Pfam (PF00252) In PDB | Oryctolagus cuniculus (rabbit) | Ribosomal protein L10 |
14 | J | 60S ribosomal protein L11 | polymer | 178 | 20288.5 | 1 | UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673) In PDB | Oryctolagus cuniculus (rabbit) | |
15 | K | 28S rRNA | polymer | 3543 | 1148115.4 | 1 | Oryctolagus cuniculus | ||
16 | L | 60S ribosomal protein L13 | polymer | 211 | 24331.7 | 1 | UniProt (G1TPV0) In PDB | Oryctolagus cuniculus (rabbit) | |
17 | M | 60S ribosomal protein L14 | polymer | 218 | 23870.5 | 1 | UniProt (G1SZ12) Pfam (PF01929) In PDB | Oryctolagus cuniculus (rabbit) | |
18 | N | Ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (G1T0C1) Pfam (PF00827) In PDB | Oryctolagus cuniculus (rabbit) | |
19 | O | 60S ribosomal protein L13 | polymer | 203 | 23533.3 | 1 | Oryctolagus cuniculus (rabbit) | ||
20 | P | uL22 | polymer | 184 | 21444.2 | 1 | UniProt (G1TVT6) Pfam (PF00237) UniProt (by SIFTS) (G1SCJ6) In PDB | Oryctolagus cuniculus (rabbit) | |
21 | Q | Ribosomal protein L26 | polymer | 187 | 21568.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
22 | R | Ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (G1TJR3) Pfam (PF01280) In PDB | Oryctolagus cuniculus (rabbit) | |
23 | S | 60S ribosomal protein L18a | polymer | 176 | 20827.6 | 1 | UniProt (A0A287APR1) Pfam (PF01775) In PDB | Oryctolagus cuniculus (rabbit) | |
24 | T | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (G1SHQ2) Pfam (PF01157) In PDB | Oryctolagus cuniculus (rabbit) | eL21 |
25 | U | Ribosomal protein L22 | polymer | 128 | 14813.0 | 1 | UniProt (G1TSG1) Pfam (PF01776) In PDB | Oryctolagus cuniculus (rabbit) | |
26 | V | Ribosomal protein L23 | polymer | 140 | 14892.5 | 1 | UniProt (G1T6D1) Pfam (PF00238) In PDB | Oryctolagus cuniculus (rabbit) | |
27 | W | Ribosomal protein L24 | polymer | 157 | 17825.1 | 1 | UniProt (G1SE28) Pfam (PF01246) In PDB | Oryctolagus cuniculus (rabbit) | eL24 |
28 | X | Ribosomal_L23eN domain-containing protein | polymer | 156 | 17768.2 | 1 | UniProt (G1SE76) Pfam (PF03939) Pfam (PF00276) In PDB | Oryctolagus cuniculus (rabbit) | uL23 |
29 | Y | Ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467) In PDB | Oryctolagus cuniculus (rabbit) | |
30 | Z | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777) In PDB | Oryctolagus cuniculus (rabbit) | |
31 | a | 60S ribosomal protein L27a | polymer | 148 | 16620.6 | 1 | UniProt (G1SNY0) Pfam (PF00828) In PDB | Oryctolagus cuniculus (rabbit) | uL15 |
32 | b | 60S ribosomal protein L29 | polymer | 226 | 24931.6 | 1 | UniProt (G1SGR6) Pfam (PF01779) In PDB | Oryctolagus cuniculus (rabbit) | eL29 |
33 | c | Large ribosomal subunit protein eL30 | polymer | 115 | 12807.1 | 1 | UniProt (G1TDL2) Pfam (PF01248) In PDB | Oryctolagus | 60S ribosomal protein L30 |
34 | d | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (G1SHG0) Pfam (PF01198) In PDB | Oryctolagus cuniculus (rabbit) | eL31 |
35 | e | Ribosomal protein L32 | polymer | 135 | 15898.9 | 1 | UniProt (G1U437) Pfam (PF01655) UniProt (by SIFTS) (G1TUN8) In PDB | Oryctolagus cuniculus (rabbit) | eL32 |
36 | f | 60S ribosomal protein L35a | polymer | 110 | 12580.8 | 1 | UniProt (G1SF08) Pfam (PF01247) In PDB | Oryctolagus cuniculus (rabbit) | eL33 |
37 | g | 60S ribosomal protein L34 | polymer | 116 | 13196.9 | 1 | UniProt (G1U945) Pfam (PF01199) UniProt (by SIFTS) (G1TXG5) In PDB | Oryctolagus cuniculus (rabbit) | eL34 |
38 | h | 60S ribosomal protein L35 | polymer | 123 | 14566.6 | 1 | UniProt (G1SIT5) Pfam (PF00831) In PDB | Oryctolagus cuniculus (rabbit) | uL29 |
39 | i | 60S ribosomal protein L36 | polymer | 105 | 12263.8 | 1 | UniProt (G1TTQ5) Pfam (PF01158) In PDB | Oryctolagus cuniculus (rabbit) | |
40 | j | Ribosomal protein L37 | polymer | 97 | 11111.0 | 1 | UniProt (U3KPD5) Pfam (PF01907) In PDB | Oryctolagus cuniculus (rabbit) | |
41 | k | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (G1U001) Pfam (PF01781) In PDB | Oryctolagus cuniculus (rabbit) | eL38 |
42 | l | 60S ribosomal protein L39-like | polymer | 51 | 6455.8 | 1 | UniProt (G1TTN1) Pfam (PF00832) In PDB | Oryctolagus cuniculus (rabbit) | eL39 |
43 | m | eL40 | polymer | 102 | 11699.8 | 1 | Oryctolagus cuniculus | ||
44 | n | 60S ribosomal protein L41 | polymer | 25 | 3473.5 | 1 | UniProt (A0A087WNH4) Pfam (PF05162) In PDB | Oryctolagus cuniculus (rabbit) | |
45 | o | 60S ribosomal protein L36a-like | polymer | 106 | 12477.0 | 1 | UniProt (G1U344) Pfam (PF00935) UniProt (by SIFTS) (G1T040) In PDB | Oryctolagus cuniculus (rabbit) | eL42 |
46 | p | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (G1SY53) Pfam (PF01780) In PDB | Oryctolagus cuniculus (rabbit) | eL43 |
47 | q | P-site tRNA | polymer | 76 | 24436.6 | 1 | Sus scrofa | ||
48 | r | 60S ribosomal protein L28 | polymer | 137 | 15783.6 | 1 | UniProt (G1U7L1) Pfam (PF01778) In PDB | Oryctolagus cuniculus (rabbit) | eL28 |
49 | u | 5S rRNA | polymer | 120 | 38691.9 | 1 | GenBank (4CXE_4) | Oryctolagus cuniculus (rabbit) | |
50 | v | 5.8S rRNA | polymer | 156 | 50143.6 | 1 | GenBank (4CXE_3) | Oryctolagus cuniculus (rabbit) | |
51 | w | Ribosomal protein L3 | polymer | 403 | 46108.0 | 1 | UniProt (G1TL06) Pfam (PF00297) In PDB | Oryctolagus cuniculus (rabbit) | uL3 |
52 | K, u, v, V, a... | MAGNESIUM ION | non-polymer | 24.3 | 218 | Chemie (MG) | |||
53 | o, p, g, j, m | ZINC ION | non-polymer | 65.4 | 5 | Chemie (ZN) |
Sequence modifications
F: 1 - 247 (UniProt: G1TUB1)
G: 1 - 319 (UniProt: G1STW0)
L: 1 - 211 (UniProt: G1TPV0)
R: 1 - 196 (UniProt: G1TJR3)
U: 1 - 128 (UniProt: G1TSG1)
k: 1 - 70 (UniProt: G1U001)
PDB | External Database | Details |
---|---|---|
Arg 61 | Gly 61 | conflict |
Arg 93 | Gly 93 | conflict |
Met 131 | Val 131 | conflict |
Ile 153 | Val 153 | conflict |
PDB | External Database | Details |
---|---|---|
Gly 244 | Cys 244 | conflict |
PDB | External Database | Details |
---|---|---|
Met 1 | Arg 5 | conflict |
Pro 3 | Leu 7 | conflict |
Ser 4 | Ala 8 | conflict |
Asn 6 | - | insertion |
Gly 7 | Ala 10 | conflict |
Ile 9 | Arg 12 | conflict |
Leu 10 | Arg 13 | conflict |
Lys 11 | Leu 14 | conflict |
Pro 12 | Ala 15 | conflict |
His 13 | Lys 16 | conflict |
Phe 14 | Ala 17 | conflict |
His 15 | Leu 18 | conflict |
Asp 17 | Phe 20 | conflict |
Trp 18 | Phe 21 | conflict |
Gln 19 | Ser 22 | conflict |
Arg 20 | Ser 23 | conflict |
Arg 21 | Ser 24 | conflict |
Ala 23 | Ile 26 | conflict |
Trp 25 | - | insertion |
Phe 26 | Leu 28 | conflict |
Asn 27 | Ala 29 | conflict |
Gln 28 | Phe 30 | conflict |
Pro 29 | Ser 31 | conflict |
Ala 30 | Phe 32 | conflict |
Arg 31 | Leu 33 | conflict |
Ile 33 | - | insertion |
Arg 34 | Thr 35 | conflict |
Arg 35 | Phe 36 | conflict |
Lys 37 | Met 38 | conflict |
Ala 38 | Gly 39 | conflict |
Arg 39 | Met 40 | conflict |
Gln 40 | Thr 41 | conflict |
Ala 41 | Gly 42 | conflict |
Arg 42 | Pro 43 | conflict |
Ala 43 | Val 44 | conflict |
Arg 44 | Ser 45 | conflict |
Arg 45 | Trp 46 | conflict |
Ile 46 | Val 47 | conflict |
Pro 48 | Asn 49 | conflict |
Arg 49 | Phe 50 | conflict |
Pro 50 | Ser 51 | conflict |
Ala 51 | Ser 52 | conflict |
Ala 52 | Ser 53 | conflict |
Gly 53 | Ala 54 | conflict |
Pro 54 | Glu 55 | conflict |
Ile 55 | Leu 56 | conflict |
Arg 56 | Ser 57 | conflict |
Ile 58 | Phe 59 | conflict |
Val 59 | Leu 60 | conflict |
Arg 60 | Gly 61 | conflict |
Cys 61 | Ala 62 | conflict |
Pro 62 | Glu 63 | conflict |
Thr 63 | Gly 64 | conflict |
Val 64 | Phe 65 | conflict |
Tyr 66 | - | insertion |
His 67 | - | insertion |
Thr 68 | Gly 67 | conflict |
Val 70 | - | insertion |
Arg 71 | - | insertion |
Ala 72 | - | insertion |
Gly 73 | - | insertion |
Gly 75 | - | insertion |
Phe 76 | Thr 70 | conflict |
Glu 80 | - | insertion |
Leu 81 | - | insertion |
Val 83 | Tyr 75 | conflict |
Ala 84 | Ser 76 | conflict |
Gly 85 | Phe 77 | conflict |
Ile 86 | Ser 78 | conflict |
His 87 | Arg 79 | conflict |
Lys 88 | Cys 80 | conflict |
Lys 89 | Thr 81 | conflict |
Val 90 | Leu 82 | conflict |
Arg 92 | - | insertion |
Thr 93 | - | insertion |
Ile 94 | Cys 84 | conflict |
Gly 95 | Arg 85 | conflict |
Ile 96 | Asp 86 | conflict |
Pro 100 | Leu 90 | conflict |
Arg 101 | Phe 91 | conflict |
Asn 104 | Arg 94 | conflict |
Lys 105 | Gly 95 | conflict |
Ser 109 | Met 99 | conflict |
Leu 110 | Pro 100 | conflict |
Gln 111 | Ile 101 | conflict |
Ala 112 | Val 102 | conflict |
Asn 113 | Arg 103 | conflict |
Val 114 | Ala 104 | conflict |
Gln 115 | Thr 105 | conflict |
Arg 116 | Phe 106 | conflict |
- | Trp 108 | deletion |
- | Met 109 | deletion |
Lys 118 | Pro 110 | conflict |
Glu 119 | Ala 111 | conflict |
Tyr 120 | Thr 112 | conflict |
Lys 123 | Ser 115 | conflict |
Leu 124 | Ser 116 | conflict |
Val 125 | Arg 117 | conflict |
Phe 127 | Lys 119 | conflict |
Lys 130 | Pro 122 | conflict |
Pro 131 | Ala 123 | conflict |
Ser 132 | Arg 124 | conflict |
Ala 133 | Thr 125 | conflict |
Pro 134 | Phe 126 | conflict |
Lys 135 | Val 127 | conflict |
Lys 136 | Trp 128 | conflict |
Gly 137 | Tyr 129 | conflict |
Asp 138 | Arg 130 | conflict |
Ser 139 | Thr 131 | conflict |
Ser 140 | Val 132 | conflict |
Ala 141 | Gly 133 | conflict |
Glu 142 | Gln 134 | conflict |
Glu 143 | Arg 135 | conflict |
Leu 144 | Thr 136 | conflict |
Lys 145 | Met 137 | conflict |
Leu 146 | Gly 138 | conflict |
Ala 147 | Arg 139 | conflict |
Thr 148 | Met 140 | conflict |
Gln 149 | Gly 141 | conflict |
Thr 151 | Ala 143 | conflict |
Gly 152 | Pro 144 | conflict |
Pro 153 | Ala 145 | conflict |
Val 154 | Asp 146 | conflict |
Met 155 | Leu 147 | conflict |
Pro 156 | Ala 148 | conflict |
Ile 157 | Arg 149 | conflict |
Asn 159 | Leu 151 | conflict |
Phe 161 | Glu 153 | conflict |
Lys 162 | Pro 154 | conflict |
Lys 163 | Gly 155 | conflict |
Glu 164 | Gly 156 | conflict |
Lys 165 | His 157 | conflict |
Arg 167 | Pro 159 | conflict |
Val 168 | Leu 160 | conflict |
Ile 169 | Pro 161 | conflict |
Thr 170 | Val 162 | conflict |
Glu 171 | Leu 163 | conflict |
Glu 172 | Val 164 | conflict |
Lys 174 | Val 166 | conflict |
Asn 175 | Arg 167 | conflict |
Phe 176 | Leu 168 | conflict |
Lys 177 | Gln 169 | conflict |
Ala 178 | Asp 170 | conflict |
Phe 179 | His 171 | conflict |
Ser 181 | Ile 173 | conflict |
Leu 182 | Pro 174 | conflict |
Arg 183 | Ala 175 | conflict |
Met 184 | Gly 176 | conflict |
Ala 185 | Arg 177 | conflict |
Arg 186 | His 178 | conflict |
Ala 187 | Gly 179 | conflict |
Asn 188 | Cys 180 | conflict |
Ala 189 | Val 181 | conflict |
Arg 190 | Leu 182 | conflict |
Phe 192 | Arg 184 | conflict |
Gly 193 | Ala 185 | conflict |
Ile 194 | Arg 186 | conflict |
Arg 195 | Thr 187 | conflict |
Ala 196 | Glu 188 | conflict |
Ala 199 | Lys 191 | conflict |
Lys 200 | Ser 192 | conflict |
Ala 202 | Pro 194 | conflict |
Ala 203 | Gln 195 | conflict |
Glu 204 | His 196 | conflict |
Gln 205 | Phe 197 | conflict |
Val 207 | Thr 199 | conflict |
Glu 208 | Gly 200 | conflict |
Lys 209 | Cys 201 | conflict |
Lys 210 | Arg 202 | conflict |
Lys 211 | His 203 | conflict |
PDB | External Database | Details |
---|---|---|
Arg 38 | Cys 38 | conflict |
Arg 64 | Gln 64 | conflict |
Thr 94 | Lys 94 | conflict |
PDB | External Database | Details |
---|---|---|
Leu 18 | Val 18 | conflict |
Gly 32 | Arg 32 | conflict |
Ala 36 | Glu 36 | conflict |
Phe 39 | Ser 39 | conflict |
Gly 54 | Arg 54 | conflict |
Val 60 | Ala 60 | conflict |
Ser 62 | Thr 62 | conflict |
Leu 63 | Ile 63 | conflict |
Arg 97 | His 97 | conflict |
Thr 106 | Ser 106 | conflict |
Glu 126 | Asp 126 | conflict |
PDB | External Database | Details |
---|---|---|
Lys 24 | Asn 24 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 51 |
Total formula weight | 2201207.6 | |
Non-Polymers* | Number of molecules | 223 |
Total formula weight | 5625.5 | |
All* | Total formula weight | 2206833.1 |