8P5D
Spraguea lophii ribosome in the closed conformation by cryo sub tomogram averaging
This is a non-PDB format compatible entry.
Replaces: 8BR3Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (L50) | RNA 28S | polymer | 2618 | 849039.8 | 1 | Spraguea lophii 42_110 | ||
| 2 | B (L70) | RNA 5S | polymer | 119 | 38356.8 | 1 | Spraguea lophii 42_110 | ||
| 3 | C (LA0) | 60S ribosomal protein L8 | polymer | 246 | 27005.5 | 1 | UniProt (S7W736) Pfam (PF00181) Pfam (PF03947) | Spraguea lophii 42_110 | |
| 4 | D (LAA) | uL15 | polymer | 147 | 16609.5 | 1 | Spraguea lophii 42_110 | ||
| 5 | E (LB0) | 60S ribosomal protein L3 | polymer | 392 | 44320.6 | 1 | UniProt (S7XFB1) Pfam (PF00297) | Spraguea lophii 42_110 | |
| 6 | F (LC0) | 60S ribosomal protein L4 | polymer | 328 | 37241.6 | 1 | UniProt (S7WCM8) Pfam (PF00573) | Spraguea lophii 42_110 | |
| 7 | G (LCC) | 60S ribosomal protein L3 | polymer | 110 | 12484.4 | 1 | UniProt (S7WAY0) Pfam (PF01248) | Spraguea lophii 42_110 | |
| 8 | H (LD0) | 60S ribosomal protein L5 | polymer | 291 | 33892.3 | 1 | UniProt (S7XIG7) Pfam (PF17144) Pfam (PF14204) | Spraguea lophii 42_110 | |
| 9 | I (LDD) | 60S ribosomal protein L31 | polymer | 110 | 12854.2 | 1 | UniProt (S7XW48) Pfam (PF01198) | Spraguea lophii 42_110 | |
| 10 | J (LE0) | 60S ribosomal protein L6 | polymer | 171 | 20220.1 | 1 | UniProt (S7W5S3) | Spraguea lophii 42_110 | |
| 11 | K (LEE) | 60S ribosomal protein L32 | polymer | 139 | 16076.0 | 1 | UniProt (S7XKE0) Pfam (PF01655) | Spraguea lophii 42_110 | |
| 12 | L (LF0) | 60S ribosomal protein L7 | polymer | 235 | 27935.6 | 1 | UniProt (S7W946) Pfam (PF00327) | Spraguea lophii 42_110 | |
| 13 | M (LFF) | 60S ribosomal protein L35a | polymer | 111 | 12758.0 | 1 | UniProt (S7W662) Pfam (PF01247) | Spraguea lophii 42_110 | |
| 14 | N (LG0) | 60S ribosomal protein L8 | polymer | 206 | 23605.0 | 1 | UniProt (S7XU63) Pfam (PF01248) | Spraguea lophii 42_110 | |
| 15 | O (LGG) | Ribosomal protein L34 | polymer | 106 | 12020.3 | 1 | UniProt (S7W7C6) Pfam (PF01199) | Spraguea lophii 42_110 | |
| 16 | P (LH0) | 60S ribosomal protein L9 | polymer | 187 | 21538.2 | 1 | UniProt (S7XRZ9) Pfam (PF00347) | Spraguea lophii 42_110 | |
| 17 | Q (LHH) | Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein | polymer | 119 | 14183.9 | 1 | UniProt (S7W7Y2) Pfam (PF00831) | Spraguea lophii 42_110 | |
| 18 | R (LI0) | S60 ribosomal protein L10 | polymer | 218 | 25142.3 | 1 | UniProt (S7WBF8) Pfam (PF00252) | Spraguea lophii 42_110 | |
| 19 | S (LII) | 60S ribosomal protein L36 | polymer | 98 | 11350.7 | 1 | UniProt (S7WED1) Pfam (PF01158) | Spraguea lophii 42_110 | |
| 20 | T (LJ0) | 60S ribosomal protein L11 | polymer | 171 | 19485.0 | 1 | UniProt (S7WB69) Pfam (PF00281) Pfam (PF00673) | Spraguea lophii 42_110 | |
| 21 | U (LJJ) | eL37 | polymer | 92 | 10517.7 | 1 | Spraguea lophii 42_110 | ||
| 22 | V (LL0) | 60S ribosomal protein L13 | polymer | 165 | 19513.1 | 1 | UniProt (S7XVM9) Pfam (PF01294) | Spraguea lophii 42_110 | |
| 23 | W (LLL) | 60S ribosomal protein L39 | polymer | 52 | 6227.6 | 1 | UniProt (S7XTP1) Pfam (PF00832) | Spraguea lophii 42_110 | |
| 24 | X (LM0) | Transposase | polymer | 115 | 13258.3 | 1 | UniProt (S7XVN9) | Spraguea lophii 42_110 | |
| 25 | Y (LMM) | Ubiquitin | polymer | 127 | 14563.9 | 1 | UniProt (S7XSQ3) Pfam (PF00240) Pfam (PF01020) | Spraguea lophii 42_110 | |
| 26 | Z (LN0) | Ribosomal protein L15 | polymer | 204 | 24200.4 | 1 | UniProt (S7W7A2) Pfam (PF00827) | Spraguea lophii 42_110 | |
| 27 | AA (LO0) | Ribosomal protein L13A | polymer | 198 | 22885.1 | 1 | UniProt (S7XUD8) Pfam (PF00572) | Spraguea lophii 42_110 | |
| 28 | BA (LOO) | 60S ribosomal protein L44 | polymer | 104 | 11990.5 | 1 | UniProt (S7XL20) Pfam (PF00935) | Spraguea lophii 42_110 | |
| 29 | CA (LP0) | 60S ribosomal protein L17 | polymer | 167 | 19114.5 | 1 | UniProt (S7WDR4) Pfam (PF00237) | Spraguea lophii 42_110 | |
| 30 | DA (LPP) | 60S ribosomal protein L37a | polymer | 89 | 10151.1 | 1 | UniProt (S7W6N9) Pfam (PF01780) | Spraguea lophii 42_110 | |
| 31 | EA (LQ0) | 60S ribosomal protein L18 | polymer | 183 | 21378.1 | 1 | UniProt (S7WAI2) Pfam (PF17135) | Spraguea lophii 42_110 | |
| 32 | FA (LR0) | 60S ribosomal protein L19 | polymer | 168 | 19550.0 | 1 | UniProt (S7WBY9) Pfam (PF01280) Pfam (PF25476) | Spraguea lophii 42_110 | |
| 33 | GA (LS0) | 60S ribosomal protein L20 | polymer | 171 | 20043.4 | 1 | UniProt (S7WAG4) Pfam (PF01775) | Spraguea lophii 42_110 | |
| 34 | HA (LT0) | 60s ribosomal protein L21 | polymer | 158 | 18344.4 | 1 | UniProt (S7W8F6) Pfam (PF01157) | Spraguea lophii 42_110 | |
| 35 | IA (LU0) | 60S ribosomal protein L22 | polymer | 113 | 12854.8 | 1 | UniProt (S7W958) Pfam (PF01776) | Spraguea lophii 42_110 | |
| 36 | JA (LV0) | Ribosomal protein L23 | polymer | 142 | 15240.0 | 1 | UniProt (S7XLC4) Pfam (PF00238) | Spraguea lophii 42_110 | |
| 37 | KA (LW0) | Ribosomal protein L24E | polymer | 131 | 15342.2 | 1 | UniProt (S7XSY2) Pfam (PF01246) | Spraguea lophii 42_110 | |
| 38 | LA (LX0) | 60S ribosomal protein L23a | polymer | 113 | 12557.9 | 1 | UniProt (S7XFW8) Pfam (PF00276) | Spraguea lophii 42_110 | |
| 39 | MA (LY0) | 60S ribosomal protein L26 | polymer | 131 | 15026.9 | 1 | UniProt (S7W884) Pfam (PF16906) Pfam (PF00467) | Spraguea lophii 42_110 | |
| 40 | NA (LZ0) | 60S ribosomal protein L27 | polymer | 153 | 18247.8 | 1 | UniProt (S7XU08) Pfam (PF01777) | Spraguea lophii 42_110 | |
| 41 | OA (MD1) | DNL-type domain-containing protein | polymer | 151 | 17595.1 | 1 | UniProt (S7W5K5) Pfam (PF05907) | Spraguea lophii 42_110 | |
| 42 | PA (S60) | RNA 16S | polymer | 1368 | 444812.5 | 1 | Spraguea lophii 42_110 | ||
| 43 | QA (SA0) | 40S ribosomal protein S0 | polymer | 233 | 26201.2 | 1 | UniProt (S7W8R1) Pfam (PF00318) | Spraguea lophii 42_110 | |
| 44 | RA (SAA) | 40S ribosomal protein S26 | polymer | 102 | 11974.1 | 1 | UniProt (S7W9M7) Pfam (PF01283) | Spraguea lophii 42_110 | |
| 45 | SA (SB0) | eS1 | polymer | 230 | 25934.7 | 1 | Spraguea lophii 42_110 | ||
| 46 | TA (SBB) | eS27 | polymer | 82 | 9189.9 | 1 | Spraguea lophii 42_110 | ||
| 47 | UA (SC0) | 40S ribosomal protein S2 | polymer | 248 | 27241.5 | 1 | UniProt (S7W7R5) Pfam (PF00333) Pfam (PF03719) | Spraguea lophii 42_110 | |
| 48 | VA (SCC) | eS28 | polymer | 65 | 7288.5 | 1 | Spraguea lophii 42_110 | ||
| 49 | WA (SD0) | 40S ribosomal protein S3 | polymer | 242 | 27516.5 | 1 | UniProt (S7WAW0) Pfam (PF00189) | Spraguea lophii 42_110 | |
| 50 | XA (SDD) | 40S ribosomal protein S29 | polymer | 65 | 7891.2 | 1 | UniProt (S7XJB1) Pfam (PF00253) | Spraguea lophii 42_110 | |
| 51 | YA (SE0) | 40S ribosomal protein S4 | polymer | 280 | 31442.2 | 1 | UniProt (S7XG51) Pfam (PF08071) Pfam (PF00900) Pfam (PF16121) | Spraguea lophii 42_110 | |
| 52 | ZA (SEE) | eS30 | polymer | 60 | 6816.0 | 1 | Spraguea lophii 42_110 | ||
| 53 | AB (SF0) | 40S ribosomal protein S5 | polymer | 195 | 21982.8 | 1 | UniProt (S7W4M9) Pfam (PF00177) | Spraguea lophii 42_110 | |
| 54 | BB (SFF) | Ubiquitin/40s ribosomal protein S27a fusion | polymer | 150 | 16937.8 | 1 | UniProt (S7W9X5) Pfam (PF00240) Pfam (PF01599) | Spraguea lophii 42_110 | |
| 55 | CB (SG0) | 40S ribosomal protein S6 | polymer | 230 | 26194.9 | 1 | UniProt (S7WDE5) Pfam (PF01092) | Spraguea lophii 42_110 | |
| 56 | DB (SGG) | Guanine nucleotide binding protein beta subunit | polymer | 326 | 36182.8 | 1 | UniProt (S7XVG3) Pfam (PF00400) | Spraguea lophii 42_110 | |
| 57 | EB (SH0) | 40S ribosomal protein S7 | polymer | 164 | 19132.0 | 1 | UniProt (S7XV29) Pfam (PF01251) | Spraguea lophii 42_110 | |
| 58 | FB (SI0) | 40S ribosomal protein S8 | polymer | 173 | 19912.1 | 1 | UniProt (S7XGW2) Pfam (PF01201) | Spraguea lophii 42_110 | |
| 59 | GB (SJ0) | 40S ribosomal protein S9 | polymer | 184 | 21366.0 | 1 | UniProt (S7W8E3) Pfam (PF01479) | Spraguea lophii 42_110 | |
| 60 | HB (SK0) | 40S ribosomal protein S10 | polymer | 107 | 12702.5 | 1 | UniProt (S7XU48) Pfam (PF03501) | Spraguea lophii 42_110 | |
| 61 | IB (SL0) | 40S ribosomal protein S11 | polymer | 155 | 18109.4 | 1 | UniProt (S7W8R0) Pfam (PF16205) Pfam (PF00366) | Spraguea lophii 42_110 | |
| 62 | JB (SM0) | 40S ribosomal protein S12 | polymer | 130 | 14343.7 | 1 | UniProt (S7W7D2) Pfam (PF01248) | Spraguea lophii 42_110 | |
| 63 | KB (SN0) | 40S ribosomal protein S13 | polymer | 143 | 16192.0 | 1 | UniProt (S7XVZ9) Pfam (PF08069) | Spraguea lophii 42_110 | |
| 64 | LB (SO0) | 40S ribosomal protein S14 | polymer | 135 | 14708.0 | 1 | UniProt (S7W6I0) Pfam (PF00411) | Spraguea lophii 42_110 | |
| 65 | MB (SP0) | Ribosomal protein S19 | polymer | 163 | 18514.6 | 1 | UniProt (S7XKY9) Pfam (PF00203) | Spraguea lophii 42_110 | |
| 66 | NB (SQ0) | 40S ribosomal protein S16 | polymer | 143 | 16415.1 | 1 | UniProt (S7WDU9) Pfam (PF00380) | Spraguea lophii 42_110 | |
| 67 | OB (SR0) | eS17 | polymer | 120 | 14055.3 | 1 | Spraguea lophii 42_110 | ||
| 68 | PB (SS0) | 40S ribosomal protein S18 | polymer | 160 | 18171.1 | 1 | UniProt (S7XJA1) Pfam (PF00416) | Spraguea lophii 42_110 | |
| 69 | QB (ST0) | 40S Ribosomal protein S19 | polymer | 143 | 16603.3 | 1 | UniProt (S7W7P5) Pfam (PF01090) | Spraguea lophii 42_110 | |
| 70 | RB (SU0) | 40S ribosomal protein S20 | polymer | 119 | 13777.1 | 1 | UniProt (S7W986) Pfam (PF00338) | Spraguea lophii 42_110 | |
| 71 | SB (SV0) | Ribosomal protein S21E | polymer | 67 | 7768.9 | 1 | UniProt (S7WAC1) Pfam (PF01249) | Spraguea lophii 42_110 | |
| 72 | TB (SW0) | 40S ribosomal protein S15A | polymer | 128 | 14620.1 | 1 | UniProt (S7XK92) Pfam (PF00410) | Spraguea lophii 42_110 | |
| 73 | UB (SX0) | uS12 | polymer | 141 | 15822.7 | 1 | Spraguea lophii 42_110 | ||
| 74 | VB (SY0) | 40s ribosomal protein s24 | polymer | 146 | 17189.9 | 1 | UniProt (S7W8J5) Pfam (PF01282) | Spraguea lophii 42_110 | |
| 75 | WB (SZ0) | 40S ribosomal protein S25 | polymer | 128 | 14777.1 | 1 | UniProt (S7WAV8) Pfam (PF03297) | Spraguea lophii 42_110 | |
| 76 | AC, BC, CC, DC, EC... (LOO, LPP, SAA, SBB, SDD...) | ZINC ION | non-polymer | 65.4 | 9 | Chemie (ZN) |
Sequence modifications
LA0: 1 - 206 (UniProt: S7W736)
LA0: 207 - 246 (PDB: 8P5D)
LHH: 1 - 69 (UniProt: S7W7Y2)
LHH: 70 - 119 (PDB: 8P5D)
LPP: 1 - 26 (PDB: 8P5D)
LPP: 27 - 89 (UniProt: S7W6N9)
SG0: 1 - 61 (PDB: 8P5D)
SG0: 62 - 230 (UniProt: S7WDE5)
| PDB | External Database | Details |
|---|---|---|
| Asn 206 | Thr 206 | conflict |
LHH: 1 - 69 (UniProt: S7W7Y2)
LHH: 70 - 119 (PDB: 8P5D)
LPP: 1 - 26 (PDB: 8P5D)
LPP: 27 - 89 (UniProt: S7W6N9)
SG0: 1 - 61 (PDB: 8P5D)
SG0: 62 - 230 (UniProt: S7WDE5)
| PDB | External Database | Details |
|---|---|---|
| Ala 171 | Gly 110 | conflict |
| Gly 173 | Asp 112 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 75 |
| Total formula weight | 2646510.0 | |
| Non-Polymers* | Number of molecules | 9 |
| Total formula weight | 588.7 | |
| All* | Total formula weight | 2647098.7 |
