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 | A (x) | Ribosomal protein uL1 | polymer | 217 | 24875.4 | 1 | UniProt (G1SKZ8) Pfam (PF00687) | Oryctolagus cuniculus (rabbit) | |
| 2 | B (5) | 28S rRNA | polymer | 3740 | 1213395.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 3 | C (8) | 5.8S rRNA | polymer | 156 | 50157.7 | 1 | GenBank (4CXE_3) | Oryctolagus cuniculus (rabbit) | |
| 4 | D (9) | 18S rRNA | polymer | 1786 | 576826.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 5 | E (A) | 60S ribosomal protein L8 | polymer | 257 | 28088.9 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 6 | F (AA) | 40S ribosomal protein SA | polymer | 295 | 32958.0 | 1 | UniProt (G1TLT8) Pfam (PF00318) Pfam (PF16122) | 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 | G (Aa) | 40S ribosomal protein S26-like | polymer | 115 | 13047.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 8 | H (B) | Ribosomal protein L3 | polymer | 403 | 46108.0 | 1 | UniProt (G1TL06) Pfam (PF00297) | Oryctolagus cuniculus (rabbit) | uL3 |
| 9 | I (BB) | 40S ribosomal protein S3a | polymer | 264 | 30002.1 | 1 | UniProt (G1SS70) Pfam (PF01015) | Oryctolagus cuniculus (rabbit) | RPS3A |
| 10 | J (Bb) | 40S ribosomal protein S27 | polymer | 84 | 9480.2 | 1 | UniProt (G1TZ76) Pfam (PF01667) | Oryctolagus cuniculus (rabbit) | |
| 11 | K (C) | 60S ribosomal protein L4 | polymer | 413 | 46401.9 | 1 | UniProt (G1SVW5) Pfam (PF00573) Pfam (PF14374) | Oryctolagus cuniculus (rabbit) | |
| 12 | L (CC) | 40S ribosomal protein S2 | polymer | 293 | 31287.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 13 | M (Cc) | 40S ribosomal protein S28 | polymer | 69 | 7855.1 | 1 | UniProt (G1TIB4) Pfam (PF01200) | Oryctolagus cuniculus (rabbit) | |
| 14 | N (D) | 60S ribosomal protein L5 | polymer | 297 | 34481.8 | 1 | UniProt (G1SYJ6) UniProt (by SIFTS) (P19949) | Oryctolagus cuniculus (rabbit) | |
| 15 | O (DD) | Ribosomal protein S3 | polymer | 243 | 26715.3 | 1 | UniProt (G1TNM3) Pfam (PF07650) Pfam (PF00189) | Oryctolagus cuniculus (rabbit) | |
| 16 | P (Dd) | 40S ribosomal protein S29 | polymer | 56 | 6690.8 | 1 | UniProt (G1U7M4) Pfam (PF00253) | Oryctolagus cuniculus (rabbit) | uS14 |
| 17 | Q (E) | 60S ribosomal protein L6 | polymer | 291 | 33028.3 | 1 | UniProt (G1SKF7) Pfam (PF03868) Pfam (PF01159) | Oryctolagus cuniculus (rabbit) | |
| 18 | R (EE) | 40S ribosomal protein S4 | polymer | 263 | 29654.9 | 1 | UniProt (G1TK17) Pfam (PF08071) Pfam (PF00900) Pfam (PF00467) Pfam (PF16121) | Oryctolagus cuniculus (rabbit) | |
| 19 | S (Ee) | 40S ribosomal protein S30 | polymer | 133 | 14498.9 | 1 | UniProt (G1T8A2) Pfam (PF00240) Pfam (PF04758) | Oryctolagus cuniculus (rabbit) | |
| 20 | T (F) | 60S ribosomal protein L7 | polymer | 249 | 29514.3 | 1 | UniProt (G1SV32) Pfam (PF08079) Pfam (PF00327) | Oryctolagus cuniculus (rabbit) | uL30 |
| 21 | U (FF) | Ribosomal protein S5 | polymer | 204 | 22913.5 | 1 | UniProt (G1TFM5) Pfam (PF00177) | Oryctolagus cuniculus (rabbit) | |
| 22 | V (G) | 60S ribosomal protein L7a | polymer | 266 | 30089.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 23 | W (GG) | 40S ribosomal protein S6 | polymer | 249 | 28751.9 | 1 | UniProt (G1TM55) Pfam (PF01092) | Oryctolagus cuniculus (rabbit) | |
| 24 | X (Gg) | RACK1 | polymer | 317 | 35115.7 | 1 | UniProt (G1SJB4) Pfam (PF00400) | Oryctolagus cuniculus (rabbit) | WD_REPEATS_REGION domain-containing protein |
| 25 | Y (H) | 60S ribosomal protein L9 | polymer | 192 | 21871.4 | 1 | UniProt (G1SWI6) Pfam (PF00347) | Oryctolagus cuniculus (rabbit) | |
| 26 | Z (HH) | 40S ribosomal protein S7 | polymer | 432 | 47356.2 | 1 | UniProt (G1SVB0) | Oryctolagus cuniculus (rabbit) | |
| 27 | AA (I) | 60S ribosomal protein L10 | polymer | 214 | 24643.1 | 1 | UniProt (B7NZQ2) Pfam (PF00252) | Oryctolagus cuniculus (rabbit) | Ribosomal protein L10 |
| 28 | BA (II) | 40S ribosomal protein S8 | polymer | 208 | 24263.4 | 1 | UniProt (G1TJW1) Pfam (PF01201) | Oryctolagus cuniculus (rabbit) | |
| 29 | CA (J) | 60S ribosomal protein L11 | polymer | 178 | 20288.5 | 1 | UniProt (G1TUB8) Pfam (PF00281) Pfam (PF00673) | Oryctolagus cuniculus (rabbit) | |
| 30 | DA (JJ) | 40S ribosomal protein S9 | polymer | 194 | 22641.6 | 1 | UniProt (B7NZS8) Pfam (PF00163) Pfam (PF01479) | Oryctolagus cuniculus (rabbit) | |
| 31 | EA (K) | 5S rRNA | polymer | 120 | 38691.9 | 1 | GenBank (4CXE_4) | Oryctolagus cuniculus (rabbit) | |
| 32 | FA (KK) | S10_plectin domain-containing protein | polymer | 165 | 18933.8 | 1 | UniProt (G1TPV3) Pfam (PF03501) | Oryctolagus cuniculus (rabbit) | eS10 |
| 33 | GA (L) | 60S ribosomal protein L13 | polymer | 211 | 24331.7 | 1 | UniProt (G1TKB3) Pfam (PF01294) | Oryctolagus cuniculus (rabbit) | L13 |
| 34 | HA (LL) | 40S ribosomal protein S11 | polymer | 158 | 18468.8 | 1 | UniProt (G1TRM4) Pfam (PF16205) Pfam (PF00366) | Oryctolagus cuniculus (rabbit) | |
| 35 | IA (M) | 60S ribosomal protein L14 | polymer | 218 | 23810.4 | 1 | UniProt (U3KNW6) Pfam (PF01929) UniProt (by SIFTS) (G1SZ12) | Oryctolagus cuniculus (rabbit) | |
| 36 | JA (N) | Ribosomal protein L15 | polymer | 204 | 24207.3 | 1 | UniProt (G1T0C1) Pfam (PF00827) | Oryctolagus cuniculus (rabbit) | |
| 37 | KA (NN) | 40S ribosomal protein S13 | polymer | 151 | 17259.4 | 1 | UniProt (G1SP51) Pfam (PF08069) Pfam (PF00312) | Oryctolagus cuniculus (rabbit) | uS15 |
| 38 | LA (O) | 60S ribosomal protein L13a | polymer | 203 | 23575.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 39 | MA (OO) | 40S ribosomal protein S14-like | polymer | 151 | 16288.7 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 40 | NA (P) | 60S ribosomal protein L17 | polymer | 187 | 21741.6 | 1 | UniProt (G1SCJ6) Pfam (PF00237) | Oryctolagus cuniculus (rabbit) | |
| 41 | OA (PP) | 40S ribosomal protein uS19 | polymer | 145 | 17049.2 | 1 | UniProt (G1U0Q2) Pfam (PF00203) | Oryctolagus cuniculus (rabbit) | |
| 42 | PA (Q) | Ribosomal protein L18 | polymer | 188 | 21699.7 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 43 | QA (QQ) | Ribosomal protein S16 | polymer | 146 | 16477.4 | 1 | UniProt (G1SGX4) Pfam (PF00380) | Oryctolagus cuniculus (rabbit) | |
| 44 | RA (R) | Ribosomal protein L19 | polymer | 196 | 23535.3 | 1 | UniProt (G1TYL6) Pfam (PF01280) UniProt (by SIFTS) (Q3T0W9) | Oryctolagus cuniculus (rabbit) | |
| 45 | SA (RR) | 40S ribosomal protein eS17 | polymer | 135 | 15552.1 | 1 | UniProt (G1TU13) Pfam (PF00833) | Oryctolagus cuniculus (rabbit) | |
| 46 | TA (S) | 60S ribosomal protein L18a | polymer | 224 | 26103.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 47 | UA (SS) | 40S ribosomal protein uS13 | polymer | 152 | 17759.8 | 1 | UniProt (G1TPG3) Pfam (PF00416) | Oryctolagus cuniculus (rabbit) | |
| 48 | VA (T) | 60S ribosomal protein L21 | polymer | 160 | 18610.0 | 1 | UniProt (G1SHQ2) Pfam (PF01157) | Oryctolagus cuniculus (rabbit) | eL21 |
| 49 | WA (TT) | 40S ribosomal protein S19 | polymer | 145 | 16106.6 | 1 | UniProt (G1TN62) Pfam (PF01090) | Oryctolagus cuniculus (rabbit) | RPS19 |
| 50 | XA (U) | 60S ribosomal protein L22-like | polymer | 141 | 16330.8 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 51 | YA (UU) | 40S ribosomal protein uS10 | polymer | 119 | 13398.8 | 1 | UniProt (G1SIZ2) Pfam (PF00338) | Oryctolagus cuniculus (rabbit) | |
| 52 | ZA (V) | Ribosomal protein L23 | polymer | 140 | 14892.5 | 1 | UniProt (G1T6D1) Pfam (PF00238) | Oryctolagus cuniculus (rabbit) | |
| 53 | AB (VV) | 40S ribosomal protein S21 | polymer | 83 | 9124.4 | 1 | Pfam (PF01249) UniProt (by SIFTS) (Q32PB8) | Oryctolagus cuniculus (rabbit) | |
| 54 | BB (W) | Ribosomal protein L24 | polymer | 157 | 17825.1 | 1 | UniProt (G1SE28) Pfam (PF01246) | Oryctolagus cuniculus (rabbit) | eL24 |
| 55 | CB (WW) | Ribosomal protein S15a | polymer | 130 | 14865.6 | 1 | UniProt (G1TG89) Pfam (PF00410) | Oryctolagus cuniculus (rabbit) | |
| 56 | DB (X) | 60S ribosomal protein L23a | polymer | 156 | 17740.2 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 57 | EB (XX) | 40S ribosomal protein S23 | polymer | 143 | 15844.7 | 1 | UniProt (G1SZ47) Pfam (PF00164) | Oryctolagus cuniculus (rabbit) | RPS23 |
| 58 | FB (Y) | Ribosomal protein L26 | polymer | 145 | 17303.4 | 1 | UniProt (G1SQH0) Pfam (PF16906) Pfam (PF00467) | Oryctolagus cuniculus (rabbit) | |
| 59 | GB (YY) | 40S ribosomal protein S24 | polymer | 133 | 15463.3 | 1 | UniProt (A0A5F9D2E6) Pfam (PF01282) | Oryctolagus cuniculus (rabbit) | |
| 60 | HB (Z) | 60S ribosomal protein L27 | polymer | 136 | 15835.8 | 1 | UniProt (G1TXF6) Pfam (PF00467) Pfam (PF01777) | Oryctolagus cuniculus (rabbit) | |
| 61 | IB (ZZ) | 40S ribosomal protein S25 | polymer | 124 | 13645.0 | 1 | UniProt (G1TDB3) Pfam (PF03297) | Oryctolagus cuniculus (rabbit) | |
| 62 | JB (a) | 60S ribosomal protein L27a | polymer | 148 | 16620.6 | 1 | UniProt (G1SNY0) Pfam (PF00828) | Oryctolagus cuniculus (rabbit) | uL15 |
| 63 | KB (b) | 60S ribosomal protein L29 | polymer | 245 | 26708.7 | 1 | UniProt (G1SGR6) Pfam (PF01779) | Oryctolagus cuniculus (rabbit) | |
| 64 | LB (c) | 60S ribosomal protein L30 | polymer | 115 | 12807.1 | 1 | UniProt (G1TDL2) Pfam (PF01248) | Oryctolagus cuniculus (rabbit) | eL30 |
| 65 | MB (d) | 60S ribosomal protein L31 | polymer | 125 | 14494.9 | 1 | UniProt (G1SHG0) Pfam (PF01198) | Oryctolagus cuniculus (rabbit) | eL31 |
| 66 | NB (e) | 60S ribosomal protein L32 | polymer | 157 | 18350.0 | 1 | UniProt (G1TUN8) Pfam (PF01655) | Oryctolagus cuniculus (rabbit) | eL32 |
| 67 | OB (f) | 60S ribosomal protein L35a | polymer | 110 | 12580.8 | 1 | UniProt (G1SF08) Pfam (PF01247) | Oryctolagus cuniculus (rabbit) | eL33 |
| 68 | PB (g) | 60S ribosomal protein L34 | polymer | 117 | 13326.1 | 1 | UniProt (G1TXG5) Pfam (PF01199) | Oryctolagus cuniculus (rabbit) | |
| 69 | QB (h) | 60S ribosomal protein L35 | polymer | 123 | 14566.6 | 1 | UniProt (G1SIT5) Pfam (PF00831) | Oryctolagus cuniculus (rabbit) | uL29 |
| 70 | RB (i) | 60S ribosomal protein L36 | polymer | 105 | 12263.8 | 1 | UniProt (G1TTQ5) Pfam (PF01158) | Oryctolagus cuniculus (rabbit) | |
| 71 | SB (j) | Ribosomal protein L37 | polymer | 97 | 11111.0 | 1 | UniProt (U3KPD5) Pfam (PF01907) | Oryctolagus cuniculus (rabbit) | |
| 72 | TB (k) | 60S ribosomal protein L38 | polymer | 70 | 8238.9 | 1 | UniProt (G1U001) Pfam (PF01781) | Oryctolagus cuniculus (rabbit) | eL38 |
| 73 | UB (l) | 60S ribosomal protein L39-like | polymer | 51 | 6455.8 | 1 | UniProt (G1TTN1) Pfam (PF00832) | Oryctolagus cuniculus (rabbit) | eL39 |
| 74 | VB (m) | Ubiquitin-60S ribosomal protein L40 | polymer | 128 | 14771.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 75 | WB (n) | 60s ribosomal protein l41 | polymer | 25 | 3473.5 | 1 | UniProt (A0A087WNH4) Pfam (PF05162) | Oryctolagus cuniculus (rabbit) | eL41 |
| 76 | XB (o) | 60S ribosomal protein L36a-like | polymer | 106 | 12477.0 | 1 | UniProt (G1U344) Pfam (PF00935) UniProt (by SIFTS) (G1T040) | Oryctolagus cuniculus (rabbit) | RPL36A |
| 77 | YB (p) | 60S ribosomal protein L37a | polymer | 92 | 10299.4 | 1 | UniProt (G1SY53) Pfam (PF01780) | Oryctolagus cuniculus (rabbit) | eL43 |
| 78 | ZB (r) | 60S ribosomal protein L28 | polymer | 137 | 15783.6 | 1 | UniProt (G1U7L1) Pfam (PF01778) | Oryctolagus cuniculus (rabbit) | eL28 |
| 79 | AC (s) | 60S ribosomal protein L10E | polymer | 318 | 34394.5 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 80 | BC (s1) | Dap1b | polymer | 109 | 12128.1 | 1 | UniProt (Q9I9N0) Pfam (PF15228) | Danio rerio (zebrafish) | Death-associated protein 1b |
| 81 | CC (t) | Eukaryotic translation initiation factor 5A-1 | polymer | 154 | 16954.3 | 1 | UniProt (P10160) Pfam (PF21485) Pfam (PF01287) | Oryctolagus cuniculus (rabbit) | eIF-5A-1,eIF-5A1,Eukaryotic initiation factor 5A isoform 1,eIF-5A,eIF-4D |
| 82 | DC (v) | Elongation factor 2 | polymer | 858 | 95605.4 | 1 | Oryctolagus cuniculus (rabbit) | ||
| 83 | EC (w) | SERPINE1 mRNA binding protein 1 | polymer | 407 | 44880.4 | 1 | UniProt (G1SW77) Pfam (PF16174) Pfam (PF04774) | Oryctolagus cuniculus (rabbit) | |
| 84 | AD, AE, AF, AG, AH... (5, v, 8, I, P...) | MAGNESIUM ION | non-polymer | 24.3 | 201 | Chemie (MG) | |||
| 85 | AK, BK, CK, DK, UJ... (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 |
|---|---|---|
| Thr 114 | Ala 114 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Met 1 | - | initiating methionine |
| 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 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 74 | His 74 | conflict |
| Arg 190 | His 190 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 38 | His 38 | conflict |
| Arg 151 | His 151 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 119 | Trp 119 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Lys 24 | Asn 24 | conflict |
| PDB | External Database | Details |
|---|---|---|
| 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 |
