9YGM
Babesia divergens ribosome structure by single-particle cryo-EM (3D class3, E-site tRNA)
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 (L3) | 5S ribosomal RNA | polymer | 122 | 39408.5 | 1 | Babesia divergens | ||
| 2 | B (LB) | 60S ribosomal protein uL2 | polymer | 257 | 27998.4 | 1 | UniProt (A0AAD9GFV9) | Babesia divergens | uL2 |
| 3 | C (LC) | 60S ribosomal protein uL3 | polymer | 395 | 44597.0 | 1 | UniProt (A0AAD9LLF8) | Babesia divergens | uL3 |
| 4 | D (LE) | 60S ribosomal protein uL5 | polymer | 171 | 19797.0 | 1 | UniProt (A0AAD9LFK3) | Babesia divergens | uL5 |
| 5 | E (LF) | 60S ribosomal protein uL6 | polymer | 190 | 21426.1 | 1 | UniProt (A0AAD9GAI9) | Babesia divergens | uL6 |
| 6 | F (LG) | 60S ribosomal protein eL6 | polymer | 212 | 23708.1 | 1 | UniProt (A0AAD9G923) | Babesia divergens | eL6 |
| 7 | G (LJ) | 60S ribosomal protein eL13 | polymer | 203 | 22948.3 | 1 | UniProt (A0AAD9GAJ7) | Babesia divergens | eL13 |
| 8 | H (LK) | 60S ribosomal protein uL14 | polymer | 139 | 14816.5 | 1 | UniProt (A0AAD9G6Q1) | Babesia divergens | uL14 |
| 9 | I (LP) | 60S ribosomal protein uL18 | polymer | 306 | 35365.9 | 1 | UniProt (A0AAD9LI25) | Babesia divergens | uL18 |
| 10 | J (LQ) | 60S ribosomal protein eL18 | polymer | 222 | 24357.9 | 1 | UniProt (A0AAD9G7R0) | Babesia divergens | eL18 |
| 11 | K (LU) | 60S ribosomal protein uL22 | polymer | 194 | 22143.1 | 1 | UniProt (A0AAD9GIZ6) | Babesia divergens | 60S ribosomal protein L17 |
| 12 | L (LV) | 60S ribosomal protein eL22 | polymer | 122 | 14211.6 | 1 | UniProt (A0AAD9GHH1) | Babesia divergens | 60S ribosomal protein L22 |
| 13 | M (LZ) | 60S ribosomal protein eL27 | polymer | 146 | 16800.0 | 1 | UniProt (A0AAD9LI24) | Babesia divergens | eL27 |
| 14 | N (La) | 60S ribosomal protein uL29 | polymer | 123 | 14473.5 | 1 | UniProt (A0AAD9GDQ8) | Babesia divergens | uL29 |
| 15 | O (Lb) | 60S ribosomal protein eL29 | polymer | 59 | 6820.0 | 1 | UniProt (A0AAD9LI35) | Babesia divergens | eL29 |
| 16 | P (Ld) | 60S ribosomal protein eL30 | polymer | 108 | 11965.1 | 1 | UniProt (A0AAD9LEI7) | Babesia divergens | eL30 |
| 17 | Q (Le) | 60S ribosomal protein eL31 | polymer | 117 | 13711.1 | 1 | UniProt (A0AAD9GDM1) | Babesia divergens | eL31 |
| 18 | R (Lf) | 60S ribosomal protein eL32 | polymer | 132 | 15497.3 | 1 | UniProt (A0AAD9LDR2) | Babesia divergens | eL32 |
| 19 | S (Lg) | 60S ribosomal protein eL33 | polymer | 115 | 13346.9 | 1 | UniProt (A0AAD9G6T1) | Babesia divergens | eL33 |
| 20 | T (LD) | 60S ribosomal protein uL4 | polymer | 360 | 39509.6 | 1 | UniProt (A0AAD9LL09) | Babesia divergens | uL4 |
| 21 | U (LI) | 60S ribosomal protein uL13 | polymer | 202 | 23326.9 | 1 | UniProt (A0AAD9GH72) | Babesia divergens | uL13 |
| 22 | V (LL) | 60S ribosomal protein eL14 | polymer | 133 | 14909.7 | 1 | UniProt (A0AAD9GCK1) | Babesia divergens | eL14 |
| 23 | W (LM) | 60S ribosomal protein uL15 | polymer | 147 | 16598.6 | 1 | UniProt (A0AAD9LED4) | Babesia divergens | uL15 |
| 24 | X (LN) | 60S ribosomal protein eL15 | polymer | 204 | 24502.1 | 1 | UniProt (A0AAD9LIN3) | Babesia divergens | |
| 25 | Y (LO) | 60S ribosomal protein uL16 | polymer | 227 | 25790.3 | 1 | UniProt (A0AAD9GFA1) | Babesia divergens | uL16 |
| 26 | Z (LR) | 60S ribosomal protein eL19 | polymer | 194 | 22632.1 | 1 | UniProt (A0AAD9GKV3) | Babesia divergens | eL19 |
| 27 | AA (LS) | 60S ribosomal protein eL20 | polymer | 188 | 21649.5 | 1 | UniProt (A0AAD9G7I0) | Babesia divergens | eL20 |
| 28 | BA (LT) | 60S ribosomal protein eL21 | polymer | 160 | 18438.7 | 1 | UniProt (A0AAD9GFV7) | Babesia divergens | eL21 |
| 29 | CA (LX) | 60S ribosomal protein uL24 | polymer | 137 | 16119.8 | 1 | UniProt (A0AAD9G6E2) | Babesia divergens | |
| 30 | DA (Lc) | 60S ribosomal protein uL30 | polymer | 259 | 30421.3 | 1 | UniProt (A0AAD9LFB9) | Babesia divergens | |
| 31 | EA (Lh) | 60S ribosomal protein eL34 | polymer | 150 | 17022.1 | 1 | UniProt (A0AAD9LHM2) | Babesia divergens | |
| 32 | FA (Li) | 60S ribosomal protein eL36 | polymer | 116 | 13093.7 | 1 | UniProt (A0AAD9GH83) | Babesia divergens | |
| 33 | GA (Lj) | 60S ribosomal protein eL37 | polymer | 98 | 10982.9 | 1 | UniProt (A0AAD9G827) | Babesia divergens | |
| 34 | HA (Lk) | 60S ribosomal protein eL38 | polymer | 70 | 8077.6 | 1 | UniProt (A0AAD9GAA9) | Babesia divergens | |
| 35 | IA (Ll) | 60S ribosomal protein eL39 | polymer | 59 | 7173.6 | 1 | UniProt (A0AAD9GHL1) | Babesia divergens | |
| 36 | JA (Lm) | 60S ribosomal protein eL40 | polymer | 55 | 6393.8 | 1 | UniProt (A0AAD9LH16) | Babesia divergens | |
| 37 | KA (Lp) | 60S ribosomal protein eL43 | polymer | 94 | 10612.4 | 1 | UniProt (A0AAD9G9R3) | Babesia divergens | |
| 38 | LA (Lo) | 60S ribosomal protein eL42 | polymer | 105 | 12011.4 | 1 | UniProt (A0AAD9LG33) | Babesia divergens | |
| 39 | MA (LH) | 60S ribosomal protein eL8 | polymer | 285 | 32208.0 | 1 | UniProt (A0AAD9GFQ9) | Babesia divergens | |
| 40 | NA (SA) | 40S ribosomal protein eS1 | polymer | 264 | 30101.5 | 1 | UniProt (A0AAD9LDG8) | Babesia divergens | |
| 41 | OA (SB) | 40S ribosomal protein uS2 | polymer | 274 | 31067.7 | 1 | UniProt (A0AAD9G821) | Babesia divergens | |
| 42 | PA (SD) | 40S ribosomal protein uS4 | polymer | 184 | 21626.4 | 1 | UniProt (A0AAD9GHC8) | Babesia divergens | |
| 43 | QA (SE) | 40S ribosomal protein eS4 | polymer | 266 | 30192.2 | 1 | UniProt (A0AAD9G6P4) | Babesia divergens | |
| 44 | RA (SF) | 40S ribosomal protein uS5 | polymer | 196 | 21103.6 | 1 | UniProt (A0AAD9GAQ1) | Babesia divergens | 40S ribosomal protein S2 |
| 45 | SA (SG) | 40S ribosomal protein eS6 | polymer | 239 | 27559.6 | 1 | UniProt (A0AAD9G7P5) | Babesia divergens | |
| 46 | TA (SI) | 40S ribosomal protein eS7 | polymer | 194 | 22070.0 | 1 | UniProt (A0AAD9G7G2) | Babesia divergens | |
| 47 | UA (SJ) | 40S ribosomal protein uS8 | polymer | 130 | 14857.5 | 1 | UniProt (A0AAD9GFS8) | Babesia divergens | |
| 48 | VA (SK) | 40S ribosomal protein eS8 | polymer | 192 | 21948.4 | 1 | UniProt (A0AAD9GEV3) | Babesia divergens | |
| 49 | WA (SP) | 40S ribosomal protein uS12 | polymer | 145 | 16201.0 | 1 | Babesia divergens | ||
| 50 | XA (ST) | 40S ribosomal protein uS15 | polymer | 151 | 17455.7 | 1 | UniProt (A0AAD9LME6) | Babesia divergens | |
| 51 | YA (SU) | 40S ribosomal protein uS17 | polymer | 156 | 18190.6 | 1 | UniProt (A0AAD9LJ91) | Babesia divergens | 40S ribosomal protein S11 |
| 52 | ZA (SY) | 40S ribosomal protein eS21 | polymer | 79 | 8720.7 | 1 | UniProt (A0AAD9G7M4) | Babesia divergens | |
| 53 | AB (Sb) | 40S ribosomal protein eS26 | polymer | 115 | 13262.6 | 1 | UniProt (A0AAD9G6Q6) | Babesia divergens | |
| 54 | BB (Sc) | 40S ribosomal protein eS27 | polymer | 82 | 9160.8 | 1 | UniProt (A0AAD9G7D5) | Babesia divergens | |
| 55 | CB (Se) | 40S ribosomal protein eS30 | polymer | 61 | 6826.0 | 1 | UniProt (A0AAD9LEP0) | Babesia divergens | |
| 56 | DB (SC) | 40S ribosomal protein uS3 | polymer | 223 | 24788.0 | 1 | UniProt (A0AAD9GHF5) | Babesia divergens | |
| 57 | EB (SH) | 40S ribosomal protein uS7 | polymer | 192 | 21552.2 | 1 | Babesia divergens | ||
| 58 | FB (SL) | 40S ribosomal protein uS9 | polymer | 149 | 16708.7 | 1 | UniProt (A0AAD9GAG7) | Babesia divergens | |
| 59 | GB (SM) | 40S ribosomal protein uS10 | polymer | 120 | 13527.6 | 1 | UniProt (A0AAD9GIF9) | Babesia divergens | 40S ribosomal protein S20 |
| 60 | HB (SQ) | 40S ribosomal protein eS12 | polymer | 135 | 14716.9 | 1 | UniProt (A0AAD9G6I1) | Babesia divergens | |
| 61 | IB (SR) | 40S ribosomal protein uS13 | polymer | 154 | 17521.5 | 1 | UniProt (A0AAD9LGT5) | Babesia divergens | |
| 62 | JB (SS) | 40S ribosomal protein uS14 | polymer | 66 | 7511.8 | 1 | UniProt (A0AAD9G696) | Babesia divergens | |
| 63 | KB (SW) | 40S ribosomal protein uS19 | polymer | 149 | 17246.5 | 1 | UniProt (A0AAD9LKW7) | Babesia divergens | |
| 64 | LB (Sd) | 40S ribosomal protein eS28 | polymer | 67 | 7500.7 | 1 | UniProt (A0AAD9LI57) | Babesia divergens | eS28 |
| 65 | MB (Sg) | Receptor for activated C kinase 1, RACK1 protein | polymer | 323 | 35573.3 | 1 | UniProt (A0AAD9GHI1) | Babesia divergens | |
| 66 | NB (SN) | 40S ribosomal protein eS10 | polymer | 113 | 13146.5 | 1 | UniProt (A0AAD9G6F1) | Babesia divergens | eS10 |
| 67 | OB (SZ) | 40S ribosomal protein eS24 | polymer | 135 | 15640.6 | 1 | UniProt (A0AAD9GHQ4) | Babesia divergens | eS24 |
| 68 | PB (Sa) | 40S ribosomal protein eS25 | polymer | 104 | 11915.3 | 1 | UniProt (A0AAD9GCU0) | Babesia divergens | eS25 |
| 69 | QB (Sf) | 40S ribosomal protein eS31 | polymer | 77 | 8897.7 | 1 | UniProt (A0AAD9G6D6) | Babesia divergens | |
| 70 | RB (Ln) | 60S ribosomal protein eL41 | polymer | 39 | 5136.3 | 1 | Babesia divergens | ||
| 71 | SB (SV) | 40S ribosomal protein eS17 | polymer | 134 | 15456.0 | 1 | Babesia divergens | ||
| 72 | TB (SO) | 40S ribosomal protein uS11 | polymer | 157 | 16683.1 | 1 | UniProt (A0AAD9GIK0) | Babesia divergens | |
| 73 | UB (L4) | 5.8S ribosomal RNA | polymer | 159 | 50963.2 | 1 | GenBank (149798938) | Babesia divergens | |
| 74 | VB (L5) | 28S ribosomal RNA | polymer | 3326 | 1073104.4 | 1 | Babesia divergens | ||
| 75 | WB (S7) | E-site tRNA | polymer | 74 | 23774.1 | 1 | Babesia divergens | ||
| 76 | XB (S1) | 18S ribosomal RNA | polymer | 1728 | 556419.7 | 1 | Babesia divergens | ||
| 77 | YB (LA) | 60S ribosomal protein uL1 | polymer | 217 | 24471.6 | 1 | UniProt (A0AAD9LDZ3) | Babesia divergens | |
| 78 | ZB (LW) | 60S ribosomal protein uL23 | polymer | 153 | 17344.5 | 1 | UniProt (A0AAD9G6J7) | Babesia divergens | uL23 |
| 79 | AC (LY) | 60S ribosomal protein eL24 | polymer | 156 | 17452.8 | 1 | UniProt (A0AAD9LE14) | Babesia divergens | eL24 |
| 80 | BC (SX) | 40S ribosomal protein eS19 | polymer | 174 | 20157.4 | 1 | UniProt (A0AAD9G7X0) | Babesia divergens | eS19 |
| 81 | AD, AE, AF, AG, AH... (L5, L3, L4, S1) | MAGNESIUM ION | non-polymer | 24.3 | 136 | Chemie (MG) PubChem (888) | |||
| 82 | DC, EC, FC, GC, HC (Lh, Lj, Lm, Lp, Lo) | ZINC ION | non-polymer | 65.4 | 5 | Chemie (ZN) PubChem (32051) | |||
| 83 | AI, BI, CI, DI, EI... (L5, S1) | POTASSIUM ION | non-polymer | 39.1 | 26 | Chemie (K) PubChem (813) | |||
| 84 | NI, OI, PI (SA, L5, S1) | water | water | 18.0 | 34 | Chemie (HOH) |
Sequence modifications
LQ: 1 - 222 (UniProt: A0AAD9G7R0)
LN: 7 - 204 (UniProt: A0AAD9LIN3)
SN: 1 - 113 (UniProt: A0AAD9G6F1)
SO: 1 - 157 (UniProt: A0AAD9GIK0)
LY: 1 - 156 (UniProt: A0AAD9LE14)
| PDB | External Database | Details |
|---|---|---|
| - | Val 122 | deletion |
| - | Asp 123 | deletion |
| - | Phe 124 | deletion |
| - | His 125 | deletion |
| - | Glu 126 | deletion |
| - | Lys 127 | deletion |
| - | Asp 128 | deletion |
| - | Met 129 | deletion |
| - | Met 130 | deletion |
| - | Met 131 | deletion |
| - | His 132 | deletion |
| - | Val 133 | deletion |
| - | Ser 134 | deletion |
| - | Thr 135 | deletion |
| - | Glu 136 | deletion |
| - | Ser 137 | deletion |
| - | Arg 138 | deletion |
| - | Arg 139 | deletion |
| - | Ser 140 | deletion |
| - | Ser 141 | deletion |
| - | Asp 142 | deletion |
| - | Ser 143 | deletion |
| - | Ala 144 | deletion |
| - | Gly 145 | deletion |
| - | Glu 146 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Met 1 | - | insertion |
| Gly 2 | - | insertion |
| Ala 3 | - | insertion |
| Tyr 4 | - | insertion |
| Arg 5 | - | insertion |
| Tyr 6 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| - | Gly 26 | deletion |
| - | Glu 27 | deletion |
| - | Leu 28 | deletion |
| - | Arg 29 | deletion |
| - | Phe 30 | deletion |
| - | Met 31 | deletion |
| - | Thr 32 | deletion |
| - | Val 33 | deletion |
| - | Leu 34 | deletion |
| - | Thr 35 | deletion |
| - | Tyr 36 | deletion |
| - | Tyr 37 | deletion |
| - | Phe 38 | deletion |
| - | Val 39 | deletion |
| - | Gly 40 | deletion |
| - | Ser 41 | deletion |
| - | Leu 42 | deletion |
| - | His 43 | deletion |
| - | Gly 44 | deletion |
| - | Arg 45 | deletion |
| - | Ala 46 | deletion |
| PDB | External Database | Details |
|---|---|---|
| Ias 144 | Asp 144 | conflict |
| PDB | External Database | Details |
|---|---|---|
| - | Val 61 | deletion |
| - | Cys 62 | deletion |
| - | Pro 63 | deletion |
| - | Lys 64 | deletion |
| - | Val 65 | deletion |
| - | Ser 66 | deletion |
| - | Cys 67 | deletion |
| - | Asn 68 | deletion |
| - | Asn 69 | deletion |
| - | Phe 70 | deletion |
| - | Ser 71 | deletion |
| - | Gln 72 | deletion |
| - | Trp 124 | deletion |
| - | Pro 125 | deletion |
| - | Ser 126 | deletion |
| - | His 127 | deletion |
| - | Asn 128 | deletion |
| - | Asn 129 | deletion |
| - | Cys 130 | deletion |
| - | Ser 131 | deletion |
| - | Ala 132 | deletion |
| - | Leu 133 | deletion |
| - | Phe 134 | deletion |
| - | Val 135 | deletion |
| - | Thr 136 | deletion |
| - | Met 137 | deletion |
| - | Val 138 | deletion |
| - | Thr 139 | deletion |
| - | Leu 140 | deletion |
| - | Thr 141 | deletion |
| - | Lys 142 | deletion |
| - | Ser 143 | deletion |
| - | Asp 144 | deletion |
| - | Ile 145 | deletion |
| - | Phe 146 | deletion |
| - | Ile 147 | deletion |
| - | Ile 148 | deletion |
| - | Leu 149 | deletion |
| - | Ala 150 | deletion |
| - | Phe 151 | deletion |
| - | Leu 152 | deletion |
| - | Ser 153 | deletion |
| - | Ser 154 | deletion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 80 |
| Total formula weight | 3132421.1 | |
| Non-Polymers* | Number of molecules | 167 |
| Total formula weight | 4649.1 | |
| All* | Total formula weight | 3137070.1 |
