9E7F
Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri
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 (2) | 5S rRNA | polymer | 129 | 41804.0 | 1 | GenBank (126248349) | Pyrobaculum calidifontis JCM 11548 | |
| 2 | B (3) | Putative signal-transduction protein with CBS domains | polymer | 655 | 72127.7 | 1 | UniProt (A3MX58) Pfam (PF00571) | Pyrobaculum calidifontis JCM 11548 | |
| 3 | C (1) | 23S rRNA | polymer | 3024 | 984007.9 | 1 | Pyrobaculum calidifontis JCM 11548 | ||
| 4 | D (4) | 16S rRNA | polymer | 1498 | 487519.9 | 1 | GenBank (343200235) | Pyrobaculum calidifontis JCM 11548 | |
| 5 | E (AA) | Large ribosomal subunit protein uL2 | polymer | 244 | 26240.3 | 1 | UniProt (A3MS41) Pfam (PF00181) Pfam (PF03947) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L2 |
| 6 | F (AB) | Large ribosomal subunit protein uL3 | polymer | 338 | 37240.5 | 1 | UniProt (A3MWI4) Pfam (PF00297) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L3 |
| 7 | G (AC) | Large ribosomal subunit protein uL4 | polymer | 285 | 31602.1 | 1 | UniProt (A3MWI5) Pfam (PF00573) | Pyrobaculum calidifontis JCM 11548 | |
| 8 | H (AD) | Large ribosomal subunit protein uL5 | polymer | 178 | 20156.9 | 1 | UniProt (A3MXP8) Pfam (PF00281) Pfam (PF00673) | Pyrobaculum calidifontis JCM 11548 | |
| 9 | I (AE) | Large ribosomal subunit protein uL6 | polymer | 196 | 21663.5 | 1 | UniProt (A3MWV5) Pfam (PF00347) | Pyrobaculum calidifontis JCM 11548 | |
| 10 | J (AF) | Large ribosomal subunit protein eL8 | polymer | 149 | 16013.7 | 1 | UniProt (A3MTA9) Pfam (PF01248) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L7Ae,Ribosomal protein L8e |
| 11 | K (AG) | Large ribosomal subunit protein uL13 | polymer | 186 | 21737.0 | 1 | UniProt (A3MXZ7) Pfam (PF00572) | Pyrobaculum calidifontis JCM 11548 | |
| 12 | L (AH) | Large ribosomal subunit protein eL13 | polymer | 157 | 17939.1 | 1 | UniProt (A3MTP8) Pfam (PF01294) | Pyrobaculum calidifontis JCM 11548 | |
| 13 | M (AI) | Large ribosomal subunit protein uL14 | polymer | 144 | 15768.4 | 1 | UniProt (A3MX34) Pfam (PF00238) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L14 |
| 14 | N, O (AJ, AK) | Large ribosomal subunit protein eL14 | polymer | 103 | 11470.5 | 2 | UniProt (A3MS76) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L14e |
| 15 | P (AL) | Large ribosomal subunit protein uL15 | polymer | 156 | 17525.4 | 1 | UniProt (A3MUZ1) Pfam (PF00828) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L15 |
| 16 | Q (AM) | 50S ribosomal protein L15e | polymer | 189 | 22623.8 | 1 | UniProt (A3MWR6) Pfam (PF00827) | Pyrobaculum calidifontis JCM 11548 | |
| 17 | R (AN) | Large ribosomal subunit protein uL16 | polymer | 178 | 19893.2 | 1 | UniProt (A3MXP3) Pfam (PF00252) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L10e |
| 18 | S (AO) | Large ribosomal subunit protein uL18 | polymer | 205 | 23424.3 | 1 | UniProt (A3MSJ3) Pfam (PF17144) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L18 |
| 19 | T (AP) | Large ribosomal subunit protein eL18 | polymer | 122 | 13224.7 | 1 | UniProt (A3MXZ6) Pfam (PF17135) | Pyrobaculum calidifontis JCM 11548 | |
| 20 | U (AQ) | Large ribosomal subunit protein eL19 | polymer | 147 | 17414.3 | 1 | UniProt (A3MSJ4) Pfam (PF01280) | Pyrobaculum calidifontis JCM 11548 | |
| 21 | V (AR) | Large ribosomal subunit protein eL20 | polymer | 78 | 8929.5 | 1 | UniProt (A3MX77) Pfam (PF01775) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L18Ae,50S ribosomal protein L20e,50S ribosomal protein LX |
| 22 | W (AS) | Large ribosomal subunit protein eL21 | polymer | 99 | 11319.3 | 1 | UniProt (A3MWX9) Pfam (PF01157) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L21e |
| 23 | X (AT) | Large ribosomal subunit protein uL22 | polymer | 184 | 21309.2 | 1 | UniProt (A3MTL6) Pfam (PF00237) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L22 |
| 24 | Y (AU) | Large ribosomal subunit protein uL23 | polymer | 81 | 9307.1 | 1 | UniProt (A3MWI6) Pfam (PF00276) | Pyrobaculum calidifontis JCM 11548 | |
| 25 | Z (AV) | Large ribosomal subunit protein uL24 | polymer | 128 | 14588.3 | 1 | UniProt (A3MWZ8) Pfam (PF16906) Pfam (PF00467) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L24 |
| 26 | AA (AW) | Large ribosomal subunit protein eL24 | polymer | 62 | 7102.5 | 1 | UniProt (A3MTA8) Pfam (PF01246) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L24e |
| 27 | BA (AX) | Large ribosomal subunit protein uL29 | polymer | 79 | 9158.9 | 1 | UniProt (A3MTL2) Pfam (PF00831) | Pyrobaculum calidifontis JCM 11548 | |
| 28 | CA (AY) | Large ribosomal subunit protein uL30 | polymer | 179 | 20287.8 | 1 | UniProt (A3MU87) Pfam (PF00327) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L30 |
| 29 | DA (AZ) | Large ribosomal subunit protein eL30 | polymer | 101 | 10886.8 | 1 | UniProt (A3MXZ2) Pfam (PF01248) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L30e |
| 30 | EA (Aa) | Large ribosomal subunit protein eL31 | polymer | 91 | 10668.6 | 1 | UniProt (A3MX75) Pfam (PF01198) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L31e |
| 31 | FA (Ab) | Large ribosomal subunit protein eL32 | polymer | 153 | 18172.6 | 1 | UniProt (A3MSJ5) Pfam (PF01655) | Pyrobaculum calidifontis JCM 11548 | |
| 32 | GA (Ac) | Large ribosomal subunit protein eL34 | polymer | 84 | 9373.1 | 1 | UniProt (A3MV68) Pfam (PF01199) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L34e |
| 33 | HA (Ad) | Large ribosomal subunit protein eL37 | polymer | 52 | 6174.3 | 1 | UniProt (A3MY38) Pfam (PF01907) | Pyrobaculum calidifontis JCM 11548 | |
| 34 | IA (Ae) | LSU ribosomal protein L38E | polymer | 67 | 7954.4 | 1 | UniProt (A3MTT1) Pfam (PF01781) | Pyrobaculum calidifontis JCM 11548 | |
| 35 | JA (Af) | Large ribosomal subunit protein eL39 | polymer | 51 | 6030.3 | 1 | UniProt (A3MUU4) Pfam (PF00832) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L39e |
| 36 | KA (Ag) | Large ribosomal subunit protein eL40 | polymer | 53 | 6356.7 | 1 | UniProt (A3MX99) Pfam (PF01020) | Pyrobaculum calidifontis JCM 11548 | 50S ribosomal protein L40e |
| 37 | LA (Ah) | eL42 | polymer | 91 | 10603.6 | 1 | Pfam (PF00935) UniProt (by SIFTS) (A3MUV1) | Pyrobaculum calidifontis JCM 11548 | |
| 38 | MA (Ai) | Large ribosomal subunit protein eL43 | polymer | 102 | 11387.5 | 1 | UniProt (A3MUM7) Pfam (PF01780) | Pyrobaculum calidifontis JCM 11548 | |
| 39 | NA (Aj) | DJ-1/PfpI domain-containing protein | polymer | 184 | 20956.4 | 1 | UniProt (A3MTM7) Pfam (PF01965) | Pyrobaculum calidifontis JCM 11548 | |
| 40 | OA (Ak) | PaREP1 domain containing protein | polymer | 93 | 10938.8 | 1 | UniProt (A3MWU0) | Pyrobaculum calidifontis JCM 11548 | |
| 41 | PA (BA) | Small ribosomal subunit protein eS1 | polymer | 222 | 24740.2 | 1 | UniProt (A3MVE0) Pfam (PF01015) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S3Ae,Ribosomal protein S1e |
| 42 | QA (BB) | Small ribosomal subunit protein uS2 | polymer | 208 | 23829.8 | 1 | UniProt (A3MS50) Pfam (PF00318) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S2 |
| 43 | RA (BC) | Small ribosomal subunit protein uS3 | polymer | 216 | 24688.2 | 1 | UniProt (A3MTL3) Pfam (PF07650) Pfam (PF00189) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S3 |
| 44 | SA (BD) | Small ribosomal subunit protein uS4 | polymer | 159 | 18516.2 | 1 | UniProt (A3MUS9) Pfam (PF01479) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S4 |
| 45 | TA (BE) | Small ribosomal subunit protein eS4 | polymer | 237 | 26774.4 | 1 | UniProt (A3MWZ7) Pfam (PF08071) Pfam (PF01479) Pfam (PF00900) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S4e |
| 46 | UA (BF) | Small ribosomal subunit protein uS5 | polymer | 202 | 22153.7 | 1 | UniProt (A3MU88) Pfam (PF00333) Pfam (PF03719) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S5 |
| 47 | VA (BG) | Small ribosomal subunit protein eS6 | polymer | 151 | 16248.0 | 1 | UniProt (A3MUD0) Pfam (PF01092) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S6e |
| 48 | WA (BH) | Small ribosomal subunit protein uS7 | polymer | 223 | 25515.7 | 1 | UniProt (A3MS29) Pfam (PF00177) | Pyrobaculum calidifontis JCM 11548 | |
| 49 | XA (BI) | Small ribosomal subunit protein uS8 | polymer | 130 | 14836.5 | 1 | UniProt (A3MSJ6) Pfam (PF00410) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S8 |
| 50 | YA (BJ) | Small ribosomal subunit protein eS8 | polymer | 131 | 14446.9 | 1 | UniProt (A3MWY2) Pfam (PF01201) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S8e |
| 51 | ZA (BK) | Small ribosomal subunit protein uS9 | polymer | 142 | 16146.2 | 1 | Pfam (PF00380) UniProt (by SIFTS) (A3MXZ8) | Pyrobaculum calidifontis JCM 11548 | |
| 52 | AB (BL) | Small ribosomal subunit protein uS10 | polymer | 106 | 12221.5 | 1 | UniProt (A3MT22) Pfam (PF00338) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S10 |
| 53 | BB (BM) | Small ribosomal subunit protein uS11 | polymer | 141 | 14984.2 | 1 | UniProt (A3MX63) Pfam (PF00411) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S11 |
| 54 | CB (BN) | Small ribosomal subunit protein uS12 | polymer | 147 | 16477.5 | 1 | UniProt (A3MXZ4) Pfam (PF00164) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S12 |
| 55 | DB (BO) | Small ribosomal subunit protein uS13 | polymer | 153 | 16758.6 | 1 | UniProt (A3MUT0) Pfam (PF00416) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S13 |
| 56 | EB (BP) | Small ribosomal subunit protein uS14 | polymer | 54 | 6429.8 | 1 | UniProt (A3MSJ7) Pfam (PF00253) | Pyrobaculum calidifontis JCM 11548 | |
| 57 | FB (BQ) | Small ribosomal subunit protein uS15 | polymer | 151 | 17587.6 | 1 | UniProt (A3MVD1) Pfam (PF08069) Pfam (PF00312) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S15 |
| 58 | GB (BR) | Small ribosomal subunit protein uS17 | polymer | 147 | 16986.3 | 1 | UniProt (A3MTT7) Pfam (PF00366) | Pyrobaculum calidifontis JCM 11548 | |
| 59 | HB (BS) | Small ribosomal subunit protein eS17 | polymer | 71 | 8082.5 | 1 | UniProt (A3MS42) Pfam (PF00833) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S17e |
| 60 | IB (BT) | Small ribosomal subunit protein uS19 | polymer | 158 | 18182.6 | 1 | UniProt (A0A831L0N9) Pfam (PF00203) UniProt (by SIFTS) (A3MTT6) | Pyrobaculum calidifontis JCM 11548 | |
| 61 | JB (BU) | Small ribosomal subunit protein eS19 | polymer | 158 | 17770.9 | 1 | UniProt (A3MUU6) Pfam (PF01090) | Pyrobaculum calidifontis JCM 11548 | |
| 62 | KB (BV) | Small ribosomal subunit protein eS24 | polymer | 128 | 14855.4 | 1 | UniProt (A3MSX4) Pfam (PF01282) | Pyrobaculum calidifontis JCM 11548 | |
| 63 | LB (BW) | SSU ribosomal protein S25E | polymer | 110 | 12477.7 | 1 | UniProt (A3MV37) Pfam (PF03297) | Pyrobaculum calidifontis JCM 11548 | |
| 64 | MB (BX) | SSU ribosomal protein S26E | polymer | 100 | 11571.9 | 1 | UniProt (A3MV49) Pfam (PF01283) | Pyrobaculum calidifontis JCM 11548 | |
| 65 | NB (BY) | Small ribosomal subunit protein eS27 | polymer | 67 | 7446.9 | 1 | UniProt (A3MUV2) Pfam (PF01667) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S27e |
| 66 | OB (BZ) | Small ribosomal subunit protein eS28 | polymer | 77 | 8576.0 | 1 | UniProt (B1Y9V2) Pfam (PF01200) | Pyrobaculum calidifontis JCM 11548 | 30S ribosomal protein S28e |
| 67 | PB (Ba) | SSU ribosomal protein S30E | polymer | 54 | 6113.1 | 1 | UniProt (A3MSW3) Pfam (PF04758) | Pyrobaculum calidifontis JCM 11548 | |
| 68 | QB (Bb) | aS35 | polymer | 68 | 7856.4 | 1 | Pyrobaculum calidifontis JCM 11548 | ||
| 69 | RB (Bc) | Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein | polymer | 65 | 6956.1 | 1 | UniProt (A3MY11) Pfam (PF07754) | Pyrobaculum calidifontis JCM 11548 | |
| 70 | AC, AD, AK, BC, BD... (1, 4, AL, AM, Ah) | SPERMINE | non-polymer | 202.3 | 64 | Chemie (SPM) | |||
| 71 | AE, AF, AG, AH, AI... (1, 4, BK, AA, AL) | MAGNESIUM ION | non-polymer | 24.3 | 251 | Chemie (MG) | |||
| 72 | BO, CO, DO, EO, FO... (BP, BR, BX, BY, Bc...) | ZINC ION | non-polymer | 65.4 | 11 | Chemie (ZN) | |||
| 73 | AP, AQ, BP, BQ, CP... (Ag, BY, Ah, BZ, BA...) | water | water | 18.0 | 6387 | Chemie (HOH) |
Sequence modifications
4: 1 - 1498 (GenBank: 343200235)
BM: 1 - 141 (UniProt: A3MX63)
BT: 1 - 158 (UniProt: A0A831L0N9)
BZ: 1 - 77 (UniProt: B1Y9V2)
| PDB | External Database | Details |
|---|---|---|
| 4ac 5 | C 5 | conflict |
| 4ac 1318 | C 1318 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ias 128 | Asp 128 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ala 6 | Gln 6 | conflict |
| Thr 19 | Ala 19 | conflict |
| Ser 28 | Thr 28 | conflict |
| Pro 43 | Ser 43 | conflict |
| Met 81 | Ala 81 | conflict |
| Cys 93 | Ser 93 | conflict |
| Arg 137 | Lys 137 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Arg 37 | Lys 37 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 70 |
| Total formula weight | 2611604.6 | |
| Non-Polymers* | Number of molecules | 326 |
| Total formula weight | 19769.8 | |
| All* | Total formula weight | 2631374.4 |
