7OYD
Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
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 | x | Ribosomal protein uL1 | polymer | 217 | 24875.4 | 1 | UniProt (G1SKZ8) Pfam (PF00687) In PDB | Oryctolagus cuniculus (rabbit) | |
2 | 5 | 28S rRNA | polymer | 3740 | 1213395.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
3 | 8 | 5.8S rRNA | polymer | 156 | 50157.7 | 1 | GenBank (4CXE_3) | Oryctolagus cuniculus (rabbit) | |
4 | 9 | 18S rRNA | polymer | 1786 | 576826.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
5 | A | 60S ribosomal protein L8 | polymer | 257 | 28088.9 | 1 | Oryctolagus cuniculus (rabbit) | ||
6 | AA | 40S ribosomal protein SA | polymer | 295 | 32958.0 | 1 | UniProt (G1TLT8) Pfam (PF00318) Pfam (PF16122) In PDB | Oryctolagus cuniculus (rabbit) | 37 kDa laminin receptor precursor,37LRP,37/67 kDa laminin receptor,LRP/LR,67 kDa laminin receptor,67LR,Laminin receptor 1,LamR,Laminin-binding protein precursor p40,LBP/p40 |
7 | Aa | 40S ribosomal protein S26-like | polymer | 115 | 13047.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
8 | B | Ribosomal protein L3 | polymer | 403 | 46108.0 | 1 | UniProt (G1TL06) Pfam (PF00297) In PDB | Oryctolagus cuniculus (rabbit) | uL3 |
9 | BB | 40S ribosomal protein S3a | polymer | 264 | 30002.1 | 1 | UniProt (G1SS70) Pfam (PF01015) In PDB | Oryctolagus cuniculus (rabbit) | RPS3A |
10 | Bb | 40S ribosomal protein S27 | polymer | 84 | 9480.2 | 1 | UniProt (G1TZ76) Pfam (PF01667) In PDB | Oryctolagus cuniculus (rabbit) | |
11 | C | 60S ribosomal protein L4 | polymer | 413 | 46401.9 | 1 | UniProt (G1SVW5) Pfam (PF00573) Pfam (PF14374) In PDB | Oryctolagus cuniculus (rabbit) | |
12 | CC | 40S ribosomal protein S2 | polymer | 293 | 31287.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
13 | Cc | 40S ribosomal protein S28 | polymer | 69 | 7855.1 | 1 | UniProt (G1TIB4) Pfam (PF01200) In PDB | Oryctolagus cuniculus (rabbit) | |
14 | D | 60S ribosomal protein L5 | polymer | 297 | 34481.8 | 1 | UniProt (G1SYJ6) UniProt (by SIFTS) (P19949) In PDB | Oryctolagus cuniculus (rabbit) | |
15 | DD | Ribosomal protein S3 | polymer | 243 | 26715.3 | 1 | UniProt (G1TNM3) Pfam (PF07650) Pfam (PF00189) In PDB | Oryctolagus cuniculus (rabbit) | |
16 | Dd | 40S ribosomal protein S29 | polymer | 56 | 6690.8 | 1 | UniProt (G1U7M4) Pfam (PF00253) In PDB | Oryctolagus cuniculus (rabbit) | uS14 |
17 | E | 60S ribosomal protein L6 | polymer | 291 | 33028.3 | 1 | UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159) In PDB | Oryctolagus cuniculus (rabbit) | |
18 | EE | 40S ribosomal protein S4 | polymer | 263 | 29654.9 | 1 | UniProt (G1TK17) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) In PDB | Oryctolagus cuniculus (rabbit) | |
19 | Ee | 40S ribosomal protein S30 | polymer | 133 | 14498.9 | 1 | UniProt (G1T8A2) Pfam (PF00240) Pfam (PF04758) In PDB | Oryctolagus cuniculus (rabbit) | |
20 | F | 60S ribosomal protein L7 | polymer | 249 | 29514.3 | 1 | UniProt (G1SV32) Pfam (PF08079) Pfam (PF00327) In PDB | Oryctolagus cuniculus (rabbit) | uL30 |
21 | FF | Ribosomal protein S5 | polymer | 204 | 22913.5 | 1 | UniProt (G1TFM5) Pfam (PF00177) In PDB | Oryctolagus cuniculus (rabbit) | |
22 | G | 60S ribosomal protein L7a | polymer | 266 | 30089.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
23 | GG | 40S ribosomal protein S6 | polymer | 249 | 28751.9 | 1 | UniProt (G1TM55) Pfam (PF01092) In PDB | Oryctolagus cuniculus (rabbit) | |
24 | Gg | RACK1 | polymer | 317 | 35115.7 | 1 | UniProt (G1SJB4) Pfam (PF00400) In PDB | Oryctolagus cuniculus (rabbit) | WD_REPEATS_REGION domain-containing protein |
25 | H | 60S ribosomal protein L9 | polymer | 192 | 21871.4 | 1 | UniProt (G1SWI6) Pfam (PF00347) In PDB | Oryctolagus cuniculus (rabbit) | |
26 | HH | 40S ribosomal protein S7 | polymer | 432 | 47356.2 | 1 | UniProt (G1SVB0) In PDB | Oryctolagus cuniculus (rabbit) | |
27 | I | 60S ribosomal protein L10 | polymer | 214 | 24643.1 | 1 | UniProt (B7NZQ2) Pfam (PF00252) In PDB | Oryctolagus cuniculus (rabbit) | Ribosomal protein L10 |
28 | II | 40S ribosomal protein S8 | polymer | 208 | 24263.4 | 1 | UniProt (G1TJW1) Pfam (PF01201) In PDB | Oryctolagus cuniculus (rabbit) | |
29 | J | 60S ribosomal protein L11 | polymer | 178 | 20288.5 | 1 | UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673) In PDB | Oryctolagus cuniculus (rabbit) | |
30 | JJ | 40S ribosomal protein S9 | polymer | 194 | 22641.6 | 1 | UniProt (B7NZS8) Pfam (PF00163) Pfam (PF01479) In PDB | Oryctolagus cuniculus (rabbit) | |
31 | K | 5S rRNA | polymer | 120 | 38691.9 | 1 | GenBank (4CXE_4) | Oryctolagus cuniculus (rabbit) | |
32 | KK | S10_plectin domain-containing protein | polymer | 165 | 18933.8 | 1 | UniProt (G1TPV3) Pfam (PF03501) In PDB | Oryctolagus cuniculus (rabbit) | eS10 |
33 | L | 60S ribosomal protein L13 | polymer | 211 | 24331.7 | 1 | UniProt (G1TKB3) Pfam (PF01294) In PDB | Oryctolagus cuniculus (rabbit) | L13 |
34 | LL | 40S ribosomal protein S11 | polymer | 158 | 18468.8 | 1 | UniProt (G1TRM4) Pfam (PF16205) Pfam (PF00366) In PDB | Oryctolagus cuniculus (rabbit) | |
35 | M | 60S ribosomal protein L14 | polymer | 218 | 23810.4 | 1 | UniProt (U3KNW6) Pfam (PF01929) UniProt (by SIFTS) (G1SZ12) In PDB | Oryctolagus cuniculus (rabbit) | |
36 | N | Ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (G1T0C1) Pfam (PF00827) In PDB | Oryctolagus cuniculus (rabbit) | |
37 | NN | 40S ribosomal protein S13 | polymer | 151 | 17259.4 | 1 | UniProt (G1SP51) Pfam (PF08069) Pfam (PF00312) In PDB | Oryctolagus cuniculus (rabbit) | uS15 |
38 | O | 60S ribosomal protein L13a | polymer | 203 | 23575.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
39 | OO | 40S ribosomal protein S14-like | polymer | 151 | 16288.7 | 1 | Oryctolagus cuniculus (rabbit) | ||
40 | P | 60S ribosomal protein L17 | polymer | 187 | 21741.6 | 1 | UniProt (G1SCJ6) Pfam (PF00237) In PDB | Oryctolagus cuniculus (rabbit) | |
41 | PP | 40S ribosomal protein uS19 | polymer | 145 | 17049.2 | 1 | UniProt (G1U0Q2) Pfam (PF00203) In PDB | Oryctolagus cuniculus (rabbit) | |
42 | Q | Ribosomal protein L18 | polymer | 188 | 21699.7 | 1 | Oryctolagus cuniculus (rabbit) | ||
43 | Ribosomal protein S16 | polymer | 146 | 16477.4 | 1 | UniProt (G1SGX4) Pfam (PF00380) In PDB | Oryctolagus cuniculus (rabbit) | ||
44 | R | Ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (G1TYL6) Pfam (PF01280) In PDB | Oryctolagus cuniculus (rabbit) | |
45 | RR | 40S ribosomal protein eS17 | polymer | 135 | 15552.1 | 1 | UniProt (G1TU13) Pfam (PF00833) In PDB | Oryctolagus cuniculus (rabbit) | |
46 | S | 60S ribosomal protein L18a | polymer | 224 | 26103.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
47 | SS | 40S ribosomal protein uS13 | polymer | 152 | 17759.8 | 1 | UniProt (G1TPG3) Pfam (PF00416) In PDB | Oryctolagus cuniculus (rabbit) | |
48 | T | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (G1SHQ2) Pfam (PF01157) In PDB | Oryctolagus cuniculus (rabbit) | eL21 |
49 | TT | 40S ribosomal protein S19 | polymer | 145 | 16106.6 | 1 | UniProt (G1TN62) Pfam (PF01090) In PDB | Oryctolagus cuniculus (rabbit) | RPS19 |
50 | U | 60S ribosomal protein L22-like | polymer | 141 | 16330.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
51 | UU | 40S ribosomal protein uS10 | polymer | 119 | 13398.8 | 1 | UniProt (G1SIZ2) Pfam (PF00338) In PDB | Oryctolagus cuniculus (rabbit) | |
52 | V | Ribosomal protein L23 | polymer | 140 | 14892.5 | 1 | UniProt (G1T6D1) Pfam (PF00238) In PDB | Oryctolagus cuniculus (rabbit) | |
53 | VV | 40S ribosomal protein S21 | polymer | 83 | 9124.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
54 | W | Ribosomal protein L24 | polymer | 157 | 17825.1 | 1 | UniProt (G1SE28) Pfam (PF01246) In PDB | Oryctolagus cuniculus (rabbit) | eL24 |
55 | WW | Ribosomal protein S15a | polymer | 130 | 14865.6 | 1 | UniProt (G1TG89) Pfam (PF00410) In PDB | Oryctolagus cuniculus (rabbit) | |
56 | X | 60S ribosomal protein L23a | polymer | 156 | 17740.2 | 1 | Oryctolagus cuniculus (rabbit) | ||
57 | XX | 40S ribosomal protein S23 | polymer | 143 | 15844.7 | 1 | UniProt (G1SZ47) Pfam (PF00164) In PDB | Oryctolagus cuniculus (rabbit) | RPS23 |
58 | Y | Ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467) In PDB | Oryctolagus cuniculus (rabbit) | |
59 | YY | 40S ribosomal protein S24 | polymer | 133 | 15463.3 | 1 | UniProt (A0A5F9D2E6) Pfam (PF01282) In PDB | Oryctolagus cuniculus (rabbit) | |
60 | Z | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777) In PDB | Oryctolagus cuniculus (rabbit) | |
61 | ZZ | 40S ribosomal protein S25 | polymer | 124 | 13645.0 | 1 | UniProt (G1TDB3) Pfam (PF03297) In PDB | Oryctolagus cuniculus (rabbit) | |
62 | a | 60S ribosomal protein L27a | polymer | 148 | 16620.6 | 1 | UniProt (G1SNY0) Pfam (PF00828) In PDB | Oryctolagus cuniculus (rabbit) | uL15 |
63 | b | 60S ribosomal protein L29 | polymer | 245 | 26708.7 | 1 | UniProt (G1SGR6) Pfam (PF01779) In PDB | Oryctolagus cuniculus (rabbit) | |
64 | c | 60S ribosomal protein L30 | polymer | 115 | 12807.1 | 1 | UniProt (G1TDL2) Pfam (PF01248) In PDB | Oryctolagus cuniculus (rabbit) | eL30 |
65 | d | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (G1SHG0) Pfam (PF01198) In PDB | Oryctolagus cuniculus (rabbit) | eL31 |
66 | e | 60S ribosomal protein L32 | polymer | 157 | 18350.0 | 1 | UniProt (G1TUN8) Pfam (PF01655) In PDB | Oryctolagus cuniculus (rabbit) | eL32 |
67 | f | 60S ribosomal protein L35a | polymer | 110 | 12580.8 | 1 | UniProt (G1SF08) Pfam (PF01247) In PDB | Oryctolagus cuniculus (rabbit) | eL33 |
68 | g | 60S ribosomal protein L34 | polymer | 117 | 13326.1 | 1 | UniProt (G1TXG5) Pfam (PF01199) In PDB | Oryctolagus cuniculus (rabbit) | |
69 | h | 60S ribosomal protein L35 | polymer | 123 | 14566.6 | 1 | UniProt (G1SIT5) Pfam (PF00831) In PDB | Oryctolagus cuniculus (rabbit) | uL29 |
70 | i | 60S ribosomal protein L36 | polymer | 105 | 12263.8 | 1 | UniProt (G1TTQ5) Pfam (PF01158) In PDB | Oryctolagus cuniculus (rabbit) | |
71 | j | Ribosomal protein L37 | polymer | 97 | 11111.0 | 1 | UniProt (U3KPD5) Pfam (PF01907) In PDB | Oryctolagus cuniculus (rabbit) | |
72 | k | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (G1U001) Pfam (PF01781) In PDB | Oryctolagus cuniculus (rabbit) | eL38 |
73 | l | 60S ribosomal protein L39-like | polymer | 51 | 6455.8 | 1 | UniProt (G1TTN1) Pfam (PF00832) In PDB | Oryctolagus cuniculus (rabbit) | eL39 |
74 | m | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14771.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
75 | n | 60s ribosomal protein l41 | polymer | 25 | 3473.5 | 1 | UniProt (A0A087WNH4) Pfam (PF05162) In PDB | Oryctolagus cuniculus (rabbit) | eL41 |
76 | o | 60S ribosomal protein L36a-like | polymer | 106 | 12477.0 | 1 | UniProt (G1U344) Pfam (PF00935) UniProt (by SIFTS) (G1T040) In PDB | Oryctolagus cuniculus (rabbit) | RPL36A |
77 | p | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (G1SY53) Pfam (PF01780) In PDB | Oryctolagus cuniculus (rabbit) | eL43 |
78 | r | 60S ribosomal protein L28 | polymer | 137 | 15783.6 | 1 | UniProt (G1U7L1) Pfam (PF01778) In PDB | Oryctolagus cuniculus (rabbit) | eL28 |
79 | s | 60S ribosomal protein L10E | polymer | 318 | 34394.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
80 | s1 | Dap1b | polymer | 109 | 12128.1 | 1 | UniProt (Q9I9N0) Pfam (PF15228) In PDB | Danio rerio (zebrafish) | Death-associated protein 1b |
81 | t | Eukaryotic translation initiation factor 5A-1 | polymer | 154 | 16954.3 | 1 | UniProt (P10160) Pfam (PF21485) Pfam (PF01287) In PDB | Oryctolagus cuniculus (rabbit) | eIF-5A-1,eIF-5A1,Eukaryotic initiation factor 5A isoform 1,eIF-5A,eIF-4D |
82 | v | Elongation factor 2 | polymer | 858 | 95605.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
83 | w | SERPINE1 mRNA binding protein 1 | polymer | 407 | 44880.4 | 1 | UniProt (G1SW77) Pfam (PF16174) Pfam (PF04774) In PDB | Oryctolagus cuniculus (rabbit) | |
84 | 5, v, 8, I, P... | MAGNESIUM ION | non-polymer | 24.3 | 201 | Chemie (MG) | |||
85 | j, m, o, p, Aa... | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) |
Sequence modifications
AA: 1 - 295 (UniProt: G1TLT8)
D: 2 - 297 (UniProt: G1SYJ6)
EE: 1 - 263 (UniProt: G1TK17)
II: 1 - 208 (UniProt: G1TJW1)
L: 1 - 211 (UniProt: G1TKB3)
R: 1 - 196 (UniProt: G1TYL6)
TT: 1 - 145 (UniProt: G1TN62)
k: 1 - 70 (UniProt: G1U001)
t: 2 - 155 (UniProt: P10160)
PDB | External Database | Details |
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Thr 114 | Ala 114 | conflict |
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Met 1 | - | initiating methionine |
PDB | External Database | Details |
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Gly 25 | Ser 25 | conflict |
Arg 51 | Lys 51 | conflict |
Thr 78 | Ala 78 | conflict |
Val 156 | Met 156 | conflict |
PDB | External Database | Details |
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Arg 47 | Gly 47 | conflict |
PDB | External Database | Details |
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Arg 74 | His 74 | conflict |
Arg 190 | His 190 | conflict |
PDB | External Database | Details |
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Arg 38 | His 38 | conflict |
Arg 151 | His 151 | conflict |
PDB | External Database | Details |
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Gly 119 | Trp 119 | conflict |
PDB | External Database | Details |
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Lys 24 | Asn 24 | conflict |
PDB | External Database | Details |
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Ser 36 | Gly 35 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 83 |
Total formula weight | 3573767.7 | |
Non-Polymers* | Number of molecules | 208 |
Total formula weight | 5343.2 | |
All* | Total formula weight | 3579110.9 |