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 | L50 | RNA 28S | polymer | 2618 | 849039.8 | 1 | Spraguea lophii 42_110 | ||
2 | L70 | RNA 5S | polymer | 119 | 38356.8 | 1 | Spraguea lophii 42_110 | ||
3 | LA0 | 60S ribosomal protein L8 | polymer | 246 | 27005.5 | 1 | UniProt (S7W736) Pfam (PF03947) In PDB | Spraguea lophii 42_110 | |
4 | LAA | uL15 | polymer | 147 | 16609.5 | 1 | Spraguea lophii 42_110 | ||
5 | LB0 | 60S ribosomal protein L3 | polymer | 392 | 44320.6 | 1 | UniProt (S7XFB1) Pfam (PF00297) In PDB | Spraguea lophii 42_110 | |
6 | LC0 | 60S ribosomal protein L4 | polymer | 328 | 37241.6 | 1 | UniProt (S7WCM8) Pfam (PF00573) In PDB | Spraguea lophii 42_110 | |
7 | LCC | 60S ribosomal protein L3 | polymer | 110 | 12484.4 | 1 | UniProt (S7WAY0) Pfam (PF01248) In PDB | Spraguea lophii 42_110 | |
8 | LD0 | 60S ribosomal protein L5 | polymer | 291 | 33892.3 | 1 | UniProt (S7XIG7) Pfam (PF17144) Pfam (PF14204) In PDB | Spraguea lophii 42_110 | |
9 | LDD | 60S ribosomal protein L31 | polymer | 110 | 12854.2 | 1 | UniProt (S7XW48) Pfam (PF01198) In PDB | Spraguea lophii 42_110 | |
10 | LE0 | 60S ribosomal protein L6 | polymer | 171 | 20220.1 | 1 | UniProt (S7W5S3) In PDB | Spraguea lophii 42_110 | |
11 | LEE | 60S ribosomal protein L32 | polymer | 139 | 16076.0 | 1 | UniProt (S7XKE0) Pfam (PF01655) In PDB | Spraguea lophii 42_110 | |
12 | LF0 | 60S ribosomal protein L7 | polymer | 235 | 27935.6 | 1 | UniProt (S7W946) Pfam (PF00327) In PDB | Spraguea lophii 42_110 | |
13 | LFF | 60S ribosomal protein L35a | polymer | 111 | 12758.0 | 1 | UniProt (S7W662) Pfam (PF01247) In PDB | Spraguea lophii 42_110 | |
14 | LG0 | 60S ribosomal protein L8 | polymer | 206 | 23605.0 | 1 | UniProt (S7XU63) Pfam (PF01248) In PDB | Spraguea lophii 42_110 | |
15 | LGG | Ribosomal protein L34 | polymer | 106 | 12020.3 | 1 | UniProt (S7W7C6) Pfam (PF01199) In PDB | Spraguea lophii 42_110 | |
16 | LH0 | 60S ribosomal protein L9 | polymer | 187 | 21538.2 | 1 | UniProt (S7XRZ9) Pfam (PF00347) In PDB | Spraguea lophii 42_110 | |
17 | 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) In PDB | Spraguea lophii 42_110 | |
18 | LI0 | S60 ribosomal protein L10 | polymer | 218 | 25142.3 | 1 | UniProt (S7WBF8) Pfam (PF00252) In PDB | Spraguea lophii 42_110 | |
19 | LII | 60S ribosomal protein L36 | polymer | 98 | 11350.7 | 1 | UniProt (S7WED1) Pfam (PF01158) In PDB | Spraguea lophii 42_110 | |
20 | LJ0 | 60S ribosomal protein L11 | polymer | 171 | 19485.0 | 1 | UniProt (S7WB69) Pfam (PF00281) Pfam (PF00673) In PDB | Spraguea lophii 42_110 | |
21 | LJJ | eL37 | polymer | 92 | 10517.7 | 1 | Spraguea lophii 42_110 | ||
22 | LL0 | 60S ribosomal protein L13 | polymer | 165 | 19513.1 | 1 | UniProt (S7XVM9) Pfam (PF01294) In PDB | Spraguea lophii 42_110 | |
23 | LLL | 60S ribosomal protein L39 | polymer | 52 | 6227.6 | 1 | UniProt (S7XTP1) Pfam (PF00832) In PDB | Spraguea lophii 42_110 | |
24 | LM0 | Transposase | polymer | 115 | 13258.3 | 1 | UniProt (S7XVN9) In PDB | Spraguea lophii 42_110 | |
25 | LMM | Ubiquitin | polymer | 127 | 14563.9 | 1 | UniProt (S7XSQ3) Pfam (PF00240) Pfam (PF01020) In PDB | Spraguea lophii 42_110 | |
26 | LN0 | Ribosomal protein L15 | polymer | 204 | 24200.4 | 1 | UniProt (S7W7A2) Pfam (PF00827) In PDB | Spraguea lophii 42_110 | |
27 | LO0 | Ribosomal protein L13A | polymer | 198 | 22885.1 | 1 | UniProt (S7XUD8) Pfam (PF00572) In PDB | Spraguea lophii 42_110 | |
28 | LOO | 60S ribosomal protein L44 | polymer | 104 | 11990.5 | 1 | UniProt (S7XL20) Pfam (PF00935) In PDB | Spraguea lophii 42_110 | |
29 | LP0 | 60S ribosomal protein L17 | polymer | 167 | 19114.5 | 1 | UniProt (S7WDR4) Pfam (PF00237) In PDB | Spraguea lophii 42_110 | |
30 | LPP | 60S ribosomal protein L37a | polymer | 89 | 10151.1 | 1 | UniProt (S7W6N9) Pfam (PF01780) In PDB | Spraguea lophii 42_110 | |
31 | LQ0 | 60S ribosomal protein L18 | polymer | 183 | 21378.1 | 1 | UniProt (S7WAI2) Pfam (PF17135) In PDB | Spraguea lophii 42_110 | |
32 | LR0 | 60S ribosomal protein L19 | polymer | 168 | 19550.0 | 1 | UniProt (S7WBY9) Pfam (PF01280) In PDB | Spraguea lophii 42_110 | |
33 | LS0 | 60S ribosomal protein L20 | polymer | 171 | 20043.4 | 1 | UniProt (S7WAG4) Pfam (PF01775) In PDB | Spraguea lophii 42_110 | |
34 | LT0 | 60s ribosomal protein L21 | polymer | 158 | 18344.4 | 1 | UniProt (S7W8F6) Pfam (PF01157) In PDB | Spraguea lophii 42_110 | |
35 | LU0 | 60S ribosomal protein L22 | polymer | 113 | 12854.8 | 1 | UniProt (S7W958) Pfam (PF01776) In PDB | Spraguea lophii 42_110 | |
36 | LV0 | Ribosomal protein L23 | polymer | 142 | 15240.0 | 1 | UniProt (S7XLC4) Pfam (PF00238) In PDB | Spraguea lophii 42_110 | |
37 | LW0 | Ribosomal protein L24E | polymer | 131 | 15342.2 | 1 | UniProt (S7XSY2) Pfam (PF01246) In PDB | Spraguea lophii 42_110 | |
38 | LX0 | 60S ribosomal protein L23a | polymer | 113 | 12557.9 | 1 | UniProt (S7XFW8) Pfam (PF00276) In PDB | Spraguea lophii 42_110 | |
39 | LY0 | 60S ribosomal protein L26 | polymer | 131 | 15026.9 | 1 | UniProt (S7W884) Pfam (PF16906) Pfam (PF00467) In PDB | Spraguea lophii 42_110 | |
40 | LZ0 | 60S ribosomal protein L27 | polymer | 153 | 18247.8 | 1 | UniProt (S7XU08) Pfam (PF01777) In PDB | Spraguea lophii 42_110 | |
41 | MD1 | DNL-type domain-containing protein | polymer | 151 | 17595.1 | 1 | UniProt (S7W5K5) Pfam (PF05907) In PDB | Spraguea lophii 42_110 | |
42 | S60 | RNA 16S | polymer | 1368 | 444812.5 | 1 | Spraguea lophii 42_110 | ||
43 | SA0 | 40S ribosomal protein S0 | polymer | 233 | 26201.2 | 1 | UniProt (S7W8R1) Pfam (PF00318) In PDB | Spraguea lophii 42_110 | |
44 | SAA | 40S ribosomal protein S26 | polymer | 102 | 11974.1 | 1 | UniProt (S7W9M7) Pfam (PF01283) In PDB | Spraguea lophii 42_110 | |
45 | SB0 | eS1 | polymer | 230 | 25934.7 | 1 | Spraguea lophii 42_110 | ||
46 | SBB | eS27 | polymer | 82 | 9189.9 | 1 | Spraguea lophii 42_110 | ||
47 | SC0 | 40S ribosomal protein S2 | polymer | 248 | 27241.5 | 1 | UniProt (S7W7R5) Pfam (PF00333) Pfam (PF03719) In PDB | Spraguea lophii 42_110 | |
48 | SCC | eS28 | polymer | 65 | 7288.5 | 1 | Spraguea lophii 42_110 | ||
49 | SD0 | 40S ribosomal protein S3 | polymer | 242 | 27516.5 | 1 | UniProt (S7WAW0) Pfam (PF00189) In PDB | Spraguea lophii 42_110 | |
50 | SDD | 40S ribosomal protein S29 | polymer | 65 | 7891.2 | 1 | UniProt (S7XJB1) Pfam (PF00253) In PDB | Spraguea lophii 42_110 | |
51 | SE0 | 40S ribosomal protein S4 | polymer | 280 | 31442.2 | 1 | UniProt (S7XG51) Pfam (PF08071) Pfam (PF00900) Pfam (PF16121) In PDB | Spraguea lophii 42_110 | |
52 | SEE | eS30 | polymer | 60 | 6816.0 | 1 | Spraguea lophii 42_110 | ||
53 | SF0 | 40S ribosomal protein S5 | polymer | 195 | 21982.8 | 1 | UniProt (S7W4M9) Pfam (PF00177) In PDB | Spraguea lophii 42_110 | |
54 | SFF | Ubiquitin/40s ribosomal protein S27a fusion | polymer | 150 | 16937.8 | 1 | UniProt (S7W9X5) Pfam (PF00240) Pfam (PF01599) In PDB | Spraguea lophii 42_110 | |
55 | SG0 | 40S ribosomal protein S6 | polymer | 230 | 26194.9 | 1 | UniProt (S7WDE5) Pfam (PF01092) In PDB | Spraguea lophii 42_110 | |
56 | SGG | Guanine nucleotide binding protein beta subunit | polymer | 326 | 36182.8 | 1 | UniProt (S7XVG3) Pfam (PF00400) In PDB | Spraguea lophii 42_110 | |
57 | SH0 | 40S ribosomal protein S7 | polymer | 164 | 19132.0 | 1 | UniProt (S7XV29) Pfam (PF01251) In PDB | Spraguea lophii 42_110 | |
58 | SI0 | 40S ribosomal protein S8 | polymer | 173 | 19912.1 | 1 | UniProt (S7XGW2) Pfam (PF01201) In PDB | Spraguea lophii 42_110 | |
59 | SJ0 | 40S ribosomal protein S9 | polymer | 184 | 21366.0 | 1 | UniProt (S7W8E3) Pfam (PF01479) In PDB | Spraguea lophii 42_110 | |
60 | SK0 | 40S ribosomal protein S10 | polymer | 107 | 12702.5 | 1 | UniProt (S7XU48) Pfam (PF03501) In PDB | Spraguea lophii 42_110 | |
61 | SL0 | 40S ribosomal protein S11 | polymer | 155 | 18109.4 | 1 | UniProt (S7W8R0) Pfam (PF16205) Pfam (PF00366) In PDB | Spraguea lophii 42_110 | |
62 | SM0 | 40S ribosomal protein S12 | polymer | 130 | 14343.7 | 1 | UniProt (S7W7D2) Pfam (PF01248) In PDB | Spraguea lophii 42_110 | |
63 | SN0 | 40S ribosomal protein S13 | polymer | 143 | 16192.0 | 1 | UniProt (S7XVZ9) Pfam (PF08069) In PDB | Spraguea lophii 42_110 | |
64 | SO0 | 40S ribosomal protein S14 | polymer | 135 | 14708.0 | 1 | UniProt (S7W6I0) Pfam (PF00411) In PDB | Spraguea lophii 42_110 | |
65 | SP0 | Ribosomal protein S19 | polymer | 163 | 18514.6 | 1 | UniProt (S7XKY9) Pfam (PF00203) In PDB | Spraguea lophii 42_110 | |
66 | SQ0 | 40S ribosomal protein S16 | polymer | 143 | 16415.1 | 1 | UniProt (S7WDU9) Pfam (PF00380) In PDB | Spraguea lophii 42_110 | |
67 | SR0 | eS17 | polymer | 120 | 14055.3 | 1 | Spraguea lophii 42_110 | ||
68 | SS0 | 40S ribosomal protein S18 | polymer | 160 | 18171.1 | 1 | UniProt (S7XJA1) Pfam (PF00416) In PDB | Spraguea lophii 42_110 | |
69 | ST0 | 40S Ribosomal protein S19 | polymer | 143 | 16603.3 | 1 | UniProt (S7W7P5) Pfam (PF01090) In PDB | Spraguea lophii 42_110 | |
70 | SU0 | 40S ribosomal protein S20 | polymer | 119 | 13777.1 | 1 | UniProt (S7W986) Pfam (PF00338) In PDB | Spraguea lophii 42_110 | |
71 | SV0 | Ribosomal protein S21E | polymer | 67 | 7768.9 | 1 | UniProt (S7WAC1) Pfam (PF01249) In PDB | Spraguea lophii 42_110 | |
72 | SW0 | 40S ribosomal protein S15A | polymer | 128 | 14620.1 | 1 | UniProt (S7XK92) Pfam (PF00410) In PDB | Spraguea lophii 42_110 | |
73 | SX0 | uS12 | polymer | 141 | 15822.7 | 1 | Spraguea lophii 42_110 | ||
74 | SY0 | 40s ribosomal protein s24 | polymer | 146 | 17189.9 | 1 | UniProt (S7W8J5) Pfam (PF01282) In PDB | Spraguea lophii 42_110 | |
75 | SZ0 | 40S ribosomal protein S25 | polymer | 128 | 14777.1 | 1 | UniProt (S7WAV8) Pfam (PF03297) In PDB | Spraguea lophii 42_110 | |
76 | 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 |