7R7A
State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
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 | 1 | 25S rRNA | polymer | 3396 | 1097532.9 | 1 | Saccharomyces cerevisiae BY4741 | ||
2 | 2 | 5.8S rRNA | polymer | 158 | 50682.9 | 1 | GenBank (1772891209) | Saccharomyces cerevisiae BY4741 | |
3 | 7 | 60S ribosomal subunit assembly/export protein LOC1 | polymer | 204 | 23652.6 | 1 | UniProt (P43586) In PDB | Saccharomyces cerevisiae BY4741 | Localization of ASH1 mRNA protein 1 |
4 | A | Ribosome biogenesis protein BRX1 | polymer | 291 | 33585.4 | 1 | UniProt (Q08235) Pfam (PF04427) In PDB | Saccharomyces cerevisiae BY4741 | |
5 | B | 60S ribosomal protein L3 | polymer | 387 | 43850.8 | 1 | UniProt (P14126) Pfam (PF00297) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1 |
6 | C | 60S ribosomal protein L4-A | polymer | 362 | 39159.1 | 1 | UniProt (P10664) Pfam (PF00573) Pfam (PF14374) In PDB | Saccharomyces cerevisiae BY4741 | L2,Large ribosomal subunit protein uL4-A,RP2,YL2 |
7 | E | 60S ribosomal protein L6-A | polymer | 175 | 19887.4 | 1 | UniProt (Q02326) Pfam (PF01159) In PDB | Saccharomyces cerevisiae BY4741 | L17,Large ribosomal subunit protein eL6-A,RP18,YL16 |
8 | F | 60S ribosomal protein L7-A | polymer | 244 | 27686.3 | 1 | UniProt (P05737) Pfam (PF08079) Pfam (PF00327) In PDB | Saccharomyces cerevisiae BY4741 | L6,Large ribosomal subunit protein uL30-A,RP11,YL8 |
9 | H | 60S ribosomal protein L9-A | polymer | 191 | 21605.1 | 1 | UniProt (P05738) Pfam (PF00347) In PDB | Saccharomyces cerevisiae BY4741 | L8,Large ribosomal subunit protein uL6-A,RP24,YL11 |
10 | J | rRNA-processing protein EBP2 | polymer | 427 | 49842.6 | 1 | UniProt (P36049) Pfam (PF05890) In PDB | Saccharomyces cerevisiae BY4741 | EBNA1-binding protein homolog |
11 | L | 60S ribosomal protein L13-A | polymer | 199 | 22604.2 | 1 | UniProt (Q12690) Pfam (PF01294) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL13-A |
12 | M | 60S ribosomal protein L14-A | polymer | 138 | 15195.1 | 1 | UniProt (P36105) Pfam (PF00467) Pfam (PF01929) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL14-A |
13 | N | 60S ribosomal protein L15-A | polymer | 204 | 24482.4 | 1 | UniProt (P05748) Pfam (PF00827) In PDB | Saccharomyces cerevisiae BY4741 | L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18 |
14 | O | 60S ribosomal protein L16-A | polymer | 199 | 22247.2 | 1 | UniProt (P26784) Pfam (PF00572) In PDB | Saccharomyces cerevisiae BY4741 | L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15 |
15 | P | 60S ribosomal protein L17-A | polymer | 184 | 20589.5 | 1 | UniProt (P05740) Pfam (PF00237) In PDB | Saccharomyces cerevisiae BY4741 | L20A,Large ribosomal subunit protein uL22-A,YL17 |
16 | Q | 60S ribosomal protein L18-A | polymer | 186 | 20609.3 | 1 | UniProt (P0CX49) Pfam (PF17135) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL18-A,RP28 |
17 | S | 60S ribosomal protein L20-A | polymer | 172 | 20478.9 | 1 | UniProt (P0CX23) Pfam (PF01775) In PDB | Saccharomyces cerevisiae BY4741 | L18a,Large ribosomal subunit protein eL20-A |
18 | T | 60S ribosomal protein L21-A | polymer | 160 | 18279.3 | 1 | UniProt (Q02753) Pfam (PF01157) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL21-A |
19 | W | Ribosome assembly factor MRT4 | polymer | 236 | 27098.0 | 1 | UniProt (P33201) Pfam (PF00466) Pfam (PF17777) In PDB | Saccharomyces cerevisiae BY4741 | mRNA turnover protein 4 |
20 | X | 60S ribosomal protein L25 | polymer | 142 | 15787.6 | 1 | UniProt (P04456) Pfam (PF03939) Pfam (PF00276) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein uL23,RP16L,YL25,YP42' |
21 | Y | 60S ribosomal protein L26-A | polymer | 127 | 14265.8 | 1 | UniProt (P05743) Pfam (PF16906) Pfam (PF00467) In PDB | Saccharomyces cerevisiae BY4741 | L33,Large ribosomal subunit protein uL24-A,YL33 |
22 | b | Nucleolar GTP-binding protein 1 | polymer | 647 | 74531.2 | 1 | UniProt (Q02892) Pfam (PF17835) Pfam (PF06858) Pfam (PF08155) In PDB | Saccharomyces cerevisiae BY4741 | |
23 | d | 60S ribosomal protein L31-A | polymer | 113 | 12980.2 | 1 | UniProt (P0C2H8) Pfam (PF01198) In PDB | Saccharomyces cerevisiae BY4741 | L34,Large ribosomal subunit protein eL31-A,YL28 |
24 | e | 60S ribosomal protein L32 | polymer | 130 | 14809.4 | 1 | UniProt (P38061) Pfam (PF01655) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL32 |
25 | f | 60S ribosomal protein L33-A | polymer | 107 | 12177.1 | 1 | UniProt (P05744) Pfam (PF01247) In PDB | Saccharomyces cerevisiae BY4741 | L37,Large ribosomal subunit protein eL33-A,RP47,YL37 |
26 | h | 60S ribosomal protein L35-A | polymer | 120 | 13942.6 | 1 | UniProt (P0CX84) Pfam (PF00831) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein uL29-A |
27 | i | 60S ribosomal protein L36-A | polymer | 100 | 11151.3 | 1 | UniProt (P05745) Pfam (PF01158) In PDB | Saccharomyces cerevisiae BY4741 | L39,Large ribosomal subunit protein eL36-A,YL39 |
28 | j | 60S ribosomal protein L37-A | polymer | 88 | 9877.4 | 1 | UniProt (P49166) Pfam (PF01907) In PDB | Saccharomyces cerevisiae BY4741 | L43,Large ribosomal subunit protein eL37-A,YL35,YP55 |
29 | l | 60S ribosome subunit biogenesis protein NIP7 | polymer | 181 | 20411.7 | 1 | UniProt (Q08962) Pfam (PF17833) Pfam (PF03657) In PDB | Saccharomyces cerevisiae BY4741 | Nuclear import protein 7 |
30 | m | Ribosome biogenesis protein ERB1 | polymer | 807 | 91772.6 | 1 | UniProt (Q04660) Pfam (PF08145) Pfam (PF00400) In PDB | Saccharomyces cerevisiae BY4741 | Eukaryotic ribosome biogenesis protein 1 |
31 | q | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | polymer | 618 | 69912.2 | 1 | UniProt (P40991) Pfam (PF01189) In PDB | Saccharomyces cerevisiae BY4741 | Nucleolar protein 2 |
32 | r | Ribosome biogenesis protein NSA2 | polymer | 261 | 29786.8 | 1 | UniProt (A6ZR80) Pfam (PF01201) UniProt (by SIFTS) (P40078) In PDB | Saccharomyces cerevisiae BY4741 | NOP7-associated protein 2 |
33 | s | Nuclear GTP-binding protein NUG1 | polymer | 520 | 57798.7 | 1 | UniProt (P40010) Pfam (PF08701) Pfam (PF01926) In PDB | Saccharomyces cerevisiae BY4741 | Nuclear GTPase 1 |
34 | u | Ribosome biogenesis protein RLP24 | polymer | 199 | 24027.7 | 1 | UniProt (Q07915) Pfam (PF01246) In PDB | Saccharomyces cerevisiae BY4741 | Ribosomal protein L24-like |
35 | v | Nucleolar protein 16 | polymer | 231 | 26954.4 | 1 | UniProt (P40007) Pfam (PF09420) In PDB | Saccharomyces cerevisiae BY4741 | |
36 | y | Eukaryotic translation initiation factor 6 | polymer | 245 | 26476.6 | 1 | UniProt (Q12522) Pfam (PF01912) In PDB | Saccharomyces cerevisiae BY4741 | eIF-6 |
37 | z | UPF0642 protein YBL028C | polymer | 106 | 12435.4 | 1 | UniProt (P38202) Pfam (PF10338) In PDB | Saccharomyces cerevisiae BY4741 | |
38 | 8 | Nucleolar complex protein 2 | polymer | 710 | 81719.3 | 1 | UniProt (P39744) Pfam (PF03715) In PDB | Saccharomyces cerevisiae BY4741 | |
39 | I | Nucleolar complex-associated protein 3 | polymer | 663 | 75689.0 | 1 | UniProt (Q07896) Pfam (PF07540) Pfam (PF03914) In PDB | Saccharomyces cerevisiae BY4741 | |
40 | K | Proteasome-interacting protein CIC1 | polymer | 376 | 42596.7 | 1 | UniProt (P38779) Pfam (PF00687) In PDB | Saccharomyces cerevisiae BY4741 | Core interacting component 1 |
41 | V | 60S ribosomal protein L23-A | polymer | 137 | 14494.0 | 1 | UniProt (P0CX41) Pfam (PF00238) In PDB | Saccharomyces cerevisiae BY4741 | L17a,Large ribosomal subunit protein uL14-A,YL32 |
42 | R | 60S ribosomal protein L19-A | polymer | 189 | 21762.3 | 1 | UniProt (P0CX82) Pfam (PF01280) In PDB | Saccharomyces cerevisiae BY4741 | L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14 |
43 | G | 60S ribosomal protein L8-A | polymer | 256 | 28175.8 | 1 | UniProt (P17076) Pfam (PF01248) In PDB | Saccharomyces cerevisiae BY4741 | L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5 |
44 | Z | 60S ribosomal protein L27-A | polymer | 136 | 15568.4 | 1 | UniProt (P0C2H6) Pfam (PF01777) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL27-A |
45 | U | 60S ribosomal protein L22-A | polymer | 121 | 13711.4 | 1 | UniProt (P05749) Pfam (PF01776) In PDB | Saccharomyces cerevisiae BY4741 | L1c,Large ribosomal subunit protein eL22-A,RP4,YL31 |
46 | c | 60S ribosomal protein L30 | polymer | 105 | 11430.4 | 1 | UniProt (P14120) Pfam (PF01248) In PDB | Saccharomyces cerevisiae BY4741 | L32,Large ribosomal subunit protein eL30,RP73,YL38 |
47 | g | 60S ribosomal protein L34-A | polymer | 121 | 13673.2 | 1 | UniProt (P87262) Pfam (PF01199) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL34-A |
48 | k | 60S ribosomal protein L38 | polymer | 78 | 8845.6 | 1 | UniProt (P49167) Pfam (PF01781) In PDB | Saccharomyces cerevisiae BY4741 | Large ribosomal subunit protein eL38 |
49 | n | Pescadillo homolog | polymer | 605 | 69984.1 | 1 | UniProt (P53261) Pfam (PF06732) Pfam (PF16589) In PDB | Saccharomyces cerevisiae BY4741 | Nucleolar protein 7,Ribosomal RNA-processing protein 13 |
50 | p | YTM1 isoform 1 | polymer | 460 | 51426.6 | 1 | UniProt (A0A8H4BV53) Pfam (PF08154) Pfam (PF00400) UniProt (by SIFTS) (Q12024) In PDB | Saccharomyces cerevisiae BY4741 | |
51 | t | Ribosome biogenesis protein RLP7 | polymer | 322 | 36621.1 | 1 | UniProt (P40693) Pfam (PF00327) In PDB | Saccharomyces cerevisiae BY4741 | Ribosomal protein L7-like |
52 | 6 | 5.8S ribosomal RNA gene and internal transcribed spacer 2 | polymer | 87 | 27786.3 | 1 | Saccharomyces cerevisiae BY4741 | ||
53 | D | ATP-dependent RNA helicase HAS1 | polymer | 505 | 56798.3 | 1 | UniProt (Q03532) Pfam (PF00270) Pfam (PF00271) Pfam (PF13959) In PDB | Saccharomyces cerevisiae BY4741 | Helicase associated with SET1 protein 1 |
54 | o | Ribosome biogenesis protein 15 | polymer | 220 | 25499.2 | 1 | UniProt (P53927) Pfam (PF00076) In PDB | Saccharomyces cerevisiae BY4741 | Nucleolar protein 15 |
55 | w | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | polymer | 841 | 96656.2 | 1 | UniProt (P25582) Pfam (PF01728) Pfam (PF11861) Pfam (PF07780) In PDB | Saccharomyces cerevisiae BY4741 | 2'-O-ribose RNA methyltransferase SPB1,AdoMet-dependent rRNA methyltransferase SPB1,S-adenosyl-L-methionine-dependent methyltransferase,Suppressor of PAB1 protein 1 |
56 | a | Ribosomal protein | polymer | 217 | 24524.8 | 1 | UniProt (A0A6A5Q2N7) Pfam (PF00687) UniProt (by SIFTS) (P0CX43) In PDB | Saccharomyces cerevisiae BY4741 | |
57 | x | ATP-dependent rRNA helicase SPB4 | polymer | 606 | 69492.2 | 1 | UniProt (A7A237) Pfam (PF00270) Pfam (PF00271) Pfam (PF13959) UniProt (by SIFTS) (P25808) In PDB | Saccharomyces cerevisiae BY4741 | Suppressor of PAB1 protein 4 |
58 | j, g | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
E: 1 - 176 (UniProt: Q02326)
m: 1 - 807 (UniProt: Q04660)
x: 1 - 606 (UniProt: A7A237)
PDB | External Database | Details |
---|---|---|
- | Leu 121 | deletion |
PDB | External Database | Details |
---|---|---|
Ala 551 | Glu 551 | conflict |
PDB | External Database | Details |
---|---|---|
Ala 405 | Thr 405 | conflict |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 57 |
Total formula weight | 2924622.3 | |
Non-Polymers* | Number of molecules | 2 |
Total formula weight | 130.8 | |
All* | Total formula weight | 2924753.1 |