6FT6
Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors
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 | 2 | 7S ribosomal RNA | polymer | 162 | 51999.8 | 1 | GenBank (1279395616) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
2 | A | 60S ribosomal protein L2-A | polymer | 254 | 27463.6 | 1 | UniProt (P0CX45) Pfam (PF00181) Pfam (PF03947) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L5,Large ribosomal subunit protein uL2-A,RP8,YL6 |
3 | B | 60S ribosomal protein L3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
4 | C | 60S ribosomal protein L4-A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
5 | D | 60S ribosomal protein L5 | polymer | 297 | 33764.8 | 1 | UniProt (P26321) Pfam (PF17144) Pfam (PF14204) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3 |
6 | E | 60S ribosomal protein L6-A | polymer | 176 | 20000.6 | 1 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
7 | F | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
8 | G | 60S ribosomal protein L8-A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
9 | H | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
10 | I | Bud site selection protein 20 | polymer | 166 | 18547.0 | 1 | UniProt (Q08004) Pfam (PF12171) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
11 | J | 60S ribosomal protein L11-A | polymer | 174 | 19755.7 | 1 | UniProt (P0C0W9) Pfam (PF00281) Pfam (PF00673) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L16,Large ribosomal subunit protein uL5-A,RP39,YL22 |
12 | L | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL13-A |
13 | M | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL14-A |
14 | N | 60S ribosomal protein L15-A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
15 | O | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
16 | P | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L20A,Large ribosomal subunit protein uL22-A,YL17 |
17 | Q | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL18-A,RP28 |
18 | R | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
19 | S | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L18a,Large ribosomal subunit protein eL20-A |
20 | T | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL21-A |
21 | U | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
22 | V | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L17a,Large ribosomal subunit protein uL14-A,YL32 |
23 | W | Ribosome assembly factor MRT4 | polymer | 236 | 27098.0 | 1 | UniProt (P33201) Pfam (PF00466) Pfam (PF17777) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | mRNA turnover protein 4 |
24 | X | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
25 | Y | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L33,Large ribosomal subunit protein uL24-A,YL33 |
26 | Z | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL27-A |
27 | a | 60S ribosomal protein L28 | polymer | 149 | 16761.7 | 1 | UniProt (P02406) Pfam (PF00828) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24 |
28 | b | Nucleolar GTP-binding protein 1 | polymer | 647 | 74531.2 | 1 | UniProt (Q02892) Pfam (PF17835) Pfam (PF06858) Pfam (PF08155) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
29 | c | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
30 | d | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L34,Large ribosomal subunit protein eL31-A,YL28 |
31 | e | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL32 |
32 | f | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
33 | g | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL34-A |
34 | h | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein uL29-A |
35 | i | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L39,Large ribosomal subunit protein eL36-A,YL39 |
36 | j | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
37 | k | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Large ribosomal subunit protein eL38 |
38 | l | 60S ribosomal protein L39 | polymer | 51 | 6358.6 | 1 | UniProt (P04650) Pfam (PF00832) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L46,Large ribosomal subunit protein eL39,YL40 |
39 | m | Nucleolar GTP-binding protein 2 | polymer | 486 | 55585.6 | 1 | UniProt (P53742) Pfam (PF08153) Pfam (PF01926) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
40 | n | Pescadillo homolog | polymer | 605 | 69984.1 | 1 | UniProt (P53261) Pfam (PF06732) Pfam (PF16589) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nucleolar protein 7,Ribosomal RNA-processing protein 13 |
41 | p | 60S ribosomal protein L43-A | polymer | 92 | 10113.0 | 1 | UniProt (P0CX25) Pfam (PF01780) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | L37a,Large ribosomal subunit protein eL43-A,YL35 |
42 | r | Ribosome biogenesis protein NSA2 | polymer | 261 | 29786.8 | 1 | UniProt (P40078) Pfam (PF01201) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | NOP7-associated protein 2 |
43 | s | Nuclear GTP-binding protein NUG1 | polymer | 520 | 57798.7 | 1 | UniProt (P40010) Pfam (PF08701) Pfam (PF01926) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nuclear GTPase 1 |
44 | u | Ribosome biogenesis protein RLP24 | polymer | 199 | 24027.7 | 1 | UniProt (Q07915) Pfam (PF01246) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Ribosomal protein L24-like |
45 | v | Ribosome biogenesis protein RPF2 | polymer | 344 | 39665.8 | 1 | UniProt (P36160) Pfam (PF04427) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
46 | w | Regulator of ribosome biosynthesis | polymer | 203 | 23001.4 | 1 | UniProt (Q08746) Pfam (PF04939) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
47 | x | Ribosome assembly protein 4 | polymer | 515 | 57106.8 | 1 | UniProt (P25382) Pfam (PF08154) Pfam (PF00400) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Notchless protein homolog 1,Ribosome biogenesis factor RSA4 |
48 | y | Eukaryotic translation initiation factor 6 | polymer | 245 | 26476.6 | 1 | UniProt (Q12522) Pfam (PF01912) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | eIF-6 |
49 | z | UPF0642 protein YBL028C | polymer | 106 | 12435.4 | 1 | UniProt (P38202) Pfam (PF10338) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
50 | 1 | 25S ribosomal RNA | polymer | 3396 | 1097493.9 | 1 | GenBank (834774822) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
51 | 3 | 5S ribosomal RNA | polymer | 121 | 38951.1 | 1 | GenBank (1329886537) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
52 | 4 | Probable metalloprotease ARX1 | polymer | 593 | 65290.3 | 1 | UniProt (Q03862) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Associated with ribosomal export complex protein 1 |
53 | 5 | rRNA-processing protein CGR1 | polymer | 120 | 14460.1 | 1 | UniProt (P53188) Pfam (PF03879) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Coiled-coil growth-regulated protein 1 |
54 | KK | Exosome complex exonuclease RRP6 | polymer | 733 | 84160.6 | 1 | UniProt (Q12149) Pfam (PF08066) Pfam (PF01612) Pfam (PF00570) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Ribosomal RNA-processing protein 6 |
55 | LL | Exosome complex protein LRP1 | polymer | 184 | 21086.3 | 1 | UniProt (P38801) Pfam (PF04000) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Like an rRNA processing protein 1,Yeast C1D domain-containing protein,rRNA processing protein 47 |
56 | MM | ATP-dependent RNA helicase DOB1 | polymer | 1011 | 115230.6 | 1 | UniProt (P47047) Pfam (PF00270) Pfam (PF00271) Pfam (PF21408) Pfam (PF13234) Pfam (PF08148) In PDB | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | mRNA transport regulator MTR4 |
57 | NN | MPP6 | polymer | 11 | 954.2 | 1 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | ||
58 | I, j, p, u | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) | |||
59 | b, m | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 2 | Chemie (GTP) | |||
60 | b, m | MAGNESIUM ION | non-polymer | 24.3 | 2 | Chemie (MG) |
Sequence modifications
2: 1 - 156 (GenBank: 1279395616)
MM: 80 - 1073 (UniProt: P47047)
PDB | External Database | Details |
---|---|---|
A 157 | - | expression tag |
A 158 | - | expression tag |
A 159 | - | expression tag |
A 160 | - | expression tag |
U 161 | - | expression tag |
U 162 | - | expression tag |
PDB | External Database | Details |
---|---|---|
Met 1 | - | initiating methionine |
Asp 2 | - | expression tag |
Ser 3 | - | expression tag |
Thr 4 | - | expression tag |
Asp 5 | - | expression tag |
Leu 6 | - | expression tag |
Phe 7 | - | expression tag |
Asp 8 | - | expression tag |
Val 9 | - | expression tag |
Phe 10 | - | expression tag |
Glu 11 | - | expression tag |
Glu 12 | - | expression tag |
Thr 13 | - | expression tag |
Pro 14 | - | expression tag |
Val 15 | - | expression tag |
Glu 16 | - | expression tag |
Leu 17 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 57 |
Total formula weight | 2669329.1 | |
Non-Polymers* | Number of molecules | 8 |
Total formula weight | 1356.6 | |
All* | Total formula weight | 2670685.7 |