8I9Z
Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4
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 | C1 | RNA (3341-MER) | polymer | 3341 | 1079977.1 | 1 | Chaetomium thermophilum | ||
2 | C2 | RNA (319-MER) | polymer | 319 | 102607.4 | 1 | Chaetomium thermophilum | ||
3 | CA | Brix domain-containing protein | polymer | 316 | 36482.0 | 1 | UniProt (G0RXZ3) Pfam (PF04427) In PDB | Chaetomium thermophilum | |
4 | CB | Ribosome biogenesis protein C8F11.04 | polymer | 391 | 43700.5 | 1 | UniProt (G0S7X0) Pfam (PF00687) In PDB | Chaetomium thermophilum | |
5 | CC | Ribosome biogenesis protein ERB1 | polymer | 801 | 90838.0 | 1 | UniProt (G0SCK6) Pfam (PF08145) Pfam (PF00400) In PDB | Chaetomium thermophilum | Eukaryotic ribosome biogenesis protein 1 |
6 | CD | Ribosome biogenesis protein YTM1 | polymer | 495 | 52989.2 | 1 | UniProt (G0SFB5) Pfam (PF00400) Pfam (PF08154) In PDB | Chaetomium thermophilum | |
7 | CE | RNA helicase | polymer | 598 | 66830.9 | 1 | UniProt (G0RYU9) Pfam (PF00270) Pfam (PF00271) Pfam (PF13959) In PDB | Chaetomium thermophilum | |
8 | CF | Ribosome assembly factor mrt4 | polymer | 270 | 30551.5 | 1 | UniProt (G0S616) Pfam (PF00466) Pfam (PF17777) In PDB | Chaetomium thermophilum | mRNA turnover protein 4 |
9 | CG | 60S ribosome subunit biogenesis protein NIP7 | polymer | 184 | 20686.0 | 1 | UniProt (G0S435) Pfam (PF17833) Pfam (PF03657) In PDB | Chaetomium thermophilum | |
10 | CH | Nucleolar GTP-binding protein 1 | polymer | 661 | 75621.5 | 1 | UniProt (G0S8F1) Pfam (PF17835) Pfam (PF06858) Pfam (PF08155) In PDB | Chaetomium thermophilum | |
11 | CI | Putative RNA-binding protein | polymer | 414 | 45884.4 | 1 | UniProt (G0S1H0) Pfam (PF00076) In PDB | Chaetomium thermophilum | |
12 | CJ | Pescadillo homolog | polymer | 679 | 77167.3 | 1 | UniProt (G0SHX6) Pfam (PF06732) Pfam (PF00533) In PDB | Chaetomium thermophilum | Nucleolar protein 7 homolog |
13 | CK | Ribosome biogenesis protein NSA2 homolog | polymer | 261 | 29724.6 | 1 | UniProt (G0S081) Pfam (PF01201) In PDB | Chaetomium thermophilum | |
14 | CL | Putative GTP binding protein | polymer | 558 | 61523.9 | 1 | UniProt (G0SEW3) Pfam (PF08701) Pfam (PF01926) In PDB | Chaetomium thermophilum | |
15 | CM, LF | 60S ribosomal protein l7-like protein | polymer | 249 | 28821.8 | 2 | UniProt (G0SFL0) Pfam (PF08079) Pfam (PF00327) In PDB | Chaetomium thermophilum | |
16 | CN | Eukaryotic translation initiation factor 6 | polymer | 246 | 26468.8 | 1 | UniProt (G0S683) Pfam (PF01912) In PDB | Chaetomium thermophilum | |
17 | CO | DUF2423 domain-containing protein | polymer | 120 | 13262.4 | 1 | UniProt (G0SHK0) Pfam (PF10338) In PDB | Chaetomium thermophilum | |
18 | CP | RNA methyltransferase nop2-like protein | polymer | 751 | 83658.3 | 1 | UniProt (G0SHQ0) Pfam (PF22458) Pfam (PF01189) In PDB | Chaetomium thermophilum | |
19 | CQ | Ribosome biogenesis protein RLP24 | polymer | 225 | 26434.3 | 1 | UniProt (G0S497) Pfam (PF01246) In PDB | Chaetomium thermophilum | |
20 | CR | Nucleolar protein 16 | polymer | 237 | 26960.5 | 1 | UniProt (G0S832) Pfam (PF09420) In PDB | Chaetomium thermophilum | |
21 | CS | AdoMet-dependent rRNA methyltransferase SPB1 | polymer | 834 | 95511.0 | 1 | UniProt (G0SGD8) Pfam (PF01728) Pfam (PF11861) Pfam (PF07780) In PDB | Chaetomium thermophilum | |
22 | CT | Nucleolar complex-associated protein 3 | polymer | 688 | 77953.9 | 1 | UniProt (G0S5L0) Pfam (PF07540) Pfam (PF03914) In PDB | Chaetomium thermophilum | |
23 | CU | rRNA-processing protein EBP2 | polymer | 451 | 50255.6 | 1 | UniProt (G0SGC2) Pfam (PF05890) In PDB | Chaetomium thermophilum | |
24 | CV | Putative 60S ribosomal protein | polymer | 147 | 15960.5 | 1 | UniProt (G0SHJ6) Pfam (PF01778) In PDB | Chaetomium thermophilum | |
25 | CW | ATP-dependent RNA helicase | polymer | 679 | 75468.5 | 1 | UniProt (G0RYG4) Pfam (PF00270) Pfam (PF00271) Pfam (PF13959) In PDB | Chaetomium thermophilum | |
26 | CX | 60S ribosomal subunit-like protein | polymer | 203 | 22678.6 | 1 | UniProt (G0SGJ0) In PDB | Chaetomium thermophilum | |
27 | CY | Putative NOC2 family protein | polymer | 788 | 89766.2 | 1 | UniProt (G0SD05) Pfam (PF03715) In PDB | Chaetomium thermophilum | |
28 | Cz | rRNA-processing protein | polymer | 123 | 14710.4 | 1 | UniProt (G0SCP3) Pfam (PF03879) In PDB | Chaetomium thermophilum | |
29 | LB | 60S ribosomal protein L3-like protein | polymer | 392 | 44456.9 | 1 | UniProt (G0RXW1) Pfam (PF00297) In PDB | Chaetomium thermophilum | |
30 | LC | 60S ribosomal protein L4-like protein | polymer | 365 | 39439.9 | 1 | UniProt (G0SFC3) Pfam (PF00573) Pfam (PF14374) In PDB | Chaetomium thermophilum | |
31 | LE | 60S ribosomal protein L6 | polymer | 200 | 22133.0 | 1 | UniProt (G0S0D6) Pfam (PF01159) In PDB | Chaetomium thermophilum | |
32 | LG | 60S ribosomal protein L8 | polymer | 262 | 29744.5 | 1 | UniProt (G0SAJ9) Pfam (PF01248) In PDB | Chaetomium thermophilum | |
33 | LH | 60S ribosomal protein l9-like protein | polymer | 192 | 21582.1 | 1 | UniProt (G0S0E5) Pfam (PF00347) In PDB | Chaetomium thermophilum | |
34 | LK | 60S ribosomal protein L12-like protein | polymer | 165 | 17802.7 | 1 | UniProt (G0SGH8) Pfam (PF03946) Pfam (PF00298) In PDB | Chaetomium thermophilum | |
35 | LL | 60S ribosomal protein L13 | polymer | 213 | 24191.2 | 1 | UniProt (G0S992) Pfam (PF01294) In PDB | Chaetomium thermophilum | |
36 | LM | 60S ribosomal protein L14-like protein | polymer | 142 | 16111.9 | 1 | UniProt (G0S1R0) Pfam (PF01929) In PDB | Chaetomium thermophilum | |
37 | LN | Ribosomal protein L15 | polymer | 203 | 24307.3 | 1 | UniProt (G0RZ88) Pfam (PF00827) In PDB | Chaetomium thermophilum | |
38 | LO | 60S ribosomal protein L16-like protein | polymer | 204 | 22993.2 | 1 | UniProt (G0SH61) Pfam (PF00572) In PDB | Chaetomium thermophilum | |
39 | LP | 60S ribosomal protein l17-like protein | polymer | 187 | 21072.2 | 1 | UniProt (G0SGY1) Pfam (PF00237) In PDB | Chaetomium thermophilum | |
40 | LQ | Ribosomal protein L18-like protein | polymer | 213 | 24195.5 | 1 | UniProt (G0S9B5) Pfam (PF17135) In PDB | Chaetomium thermophilum | |
41 | LR | Ribosomal protein L19 | polymer | 2898 | 317092.3 | 1 | UniProt (G0S9T3) Pfam (PF12074) Pfam (PF13513) Pfam (PF21040) Pfam (PF10274) Pfam (PF01280) In PDB | Chaetomium thermophilum | |
42 | LS | 60S ribosomal protein L20 | polymer | 174 | 20341.9 | 1 | UniProt (G0SCE2) Pfam (PF01775) In PDB | Chaetomium thermophilum | |
43 | LT | 60S ribosomal protein l21-like protein | polymer | 160 | 18159.2 | 1 | UniProt (G0S0Z3) Pfam (PF01157) In PDB | Chaetomium thermophilum | |
44 | LU | 60S ribosomal protein L22-like protein | polymer | 127 | 14302.6 | 1 | UniProt (G0SDS8) Pfam (PF01776) In PDB | Chaetomium thermophilum | |
45 | LV | 60S ribosomal protein l23-like protein | polymer | 139 | 14674.4 | 1 | UniProt (G0SI44) Pfam (PF00238) In PDB | Chaetomium thermophilum | |
46 | LX | 60S ribosomal protein L25-like protein | polymer | 156 | 17175.3 | 1 | UniProt (G0S507) Pfam (PF03939) Pfam (PF00276) In PDB | Chaetomium thermophilum | |
47 | LY | 60S ribosomal protein L26-like protein | polymer | 138 | 15565.3 | 1 | UniProt (G0RYN9) Pfam (PF16906) Pfam (PF00467) In PDB | Chaetomium thermophilum | |
48 | LZ | 60S ribosomal protein L27 | polymer | 135 | 15803.7 | 1 | UniProt (G0RZE9) Pfam (PF01777) In PDB | Chaetomium thermophilum | |
49 | Lc | 60S ribosomal protein l30-like protein | polymer | 108 | 11602.6 | 1 | UniProt (G0SEI0) Pfam (PF01248) In PDB | Chaetomium thermophilum | |
50 | Ld | Putative 60S ribosomal protein | polymer | 120 | 13872.2 | 1 | UniProt (G0SD68) Pfam (PF01198) In PDB | Chaetomium thermophilum | |
51 | Le | 60S ribosomal protein L32-like protein | polymer | 131 | 15096.0 | 1 | UniProt (G0S6V4) Pfam (PF01655) In PDB | Chaetomium thermophilum | |
52 | Lf | 60S ribosomal protein l33-like protein | polymer | 109 | 12330.3 | 1 | UniProt (G0SCL3) Pfam (PF01247) In PDB | Chaetomium thermophilum | |
53 | Lg | Ribosomal protein l34-like protein | polymer | 119 | 13493.0 | 1 | UniProt (G0SFN0) Pfam (PF01199) In PDB | Chaetomium thermophilum | |
54 | Lh | dolichyl-diphosphooligosaccharide--protein glycotransferase | polymer | 935 | 105169.2 | 1 | UniProt (G0S0D7) Pfam (PF00831) Pfam (PF02516) Pfam (PF21436) In PDB | Chaetomium thermophilum | |
55 | Li | 60S ribosomal protein L36 | polymer | 110 | 12784.1 | 1 | UniProt (G0SBN1) Pfam (PF01158) In PDB | Chaetomium thermophilum | |
56 | Lj | Ribosomal protein L37 | polymer | 95 | 10660.5 | 1 | UniProt (G0S101) Pfam (PF01907) In PDB | Chaetomium thermophilum | |
57 | Lk | 60S ribosomal protein L38-like protein | polymer | 81 | 9521.3 | 1 | UniProt (G0SG89) Pfam (PF01781) In PDB | Chaetomium thermophilum | |
58 | Ll | 60S ribosomal protein L39 | polymer | 51 | 6297.5 | 1 | UniProt (Q2H9R2) Pfam (PF00832) In PDB | Chaetomium thermophilum | |
59 | Lq | Ribosomal protein | polymer | 217 | 24055.3 | 1 | UniProt (G0S4Z9) Pfam (PF00687) In PDB | Chaetomium thermophilum | |
60 | CH | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
61 | CQ, Lj | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
62 | CW | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) | |||
63 | CW | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) |
Sequence modifications
CD: 1 - 495 (UniProt: G0SFB5)
CE: 1 - 598 (UniProt: G0RYU9)
CF: 1 - 270 (UniProt: G0S616)
CL: 1 - 558 (UniProt: G0SEW3)
LH: 1 - 192 (UniProt: G0S0E5)
Lk: 1 - 81 (UniProt: G0SG89)
PDB | External Database | Details |
---|---|---|
Asp 88 | Glu 88 | conflict |
PDB | External Database | Details |
---|---|---|
Lys 543 | - | insertion |
Ser 544 | - | insertion |
Phe 545 | - | insertion |
Gly 546 | - | insertion |
Phe 547 | - | insertion |
Ser 548 | - | insertion |
Thr 549 | - | insertion |
Pro 550 | - | insertion |
Pro 551 | - | insertion |
Arg 552 | - | insertion |
Val 553 | - | insertion |
Asp 554 | - | insertion |
Ile 555 | - | insertion |
Thr 556 | - | insertion |
Leu 557 | - | insertion |
Ser 558 | - | insertion |
Ala 559 | - | insertion |
Ser 560 | - | insertion |
Leu 561 | - | insertion |
Ser 562 | - | insertion |
Arg 563 | - | insertion |
Asp 564 | - | insertion |
Lys 565 | - | insertion |
Lys 566 | - | insertion |
Pro 567 | - | insertion |
Gln 568 | - | insertion |
Gly 569 | - | insertion |
Arg 570 | - | insertion |
Arg 571 | - | insertion |
Ala 572 | - | insertion |
Tyr 573 | - | insertion |
Gly 574 | - | insertion |
Ser 575 | - | insertion |
Gln 576 | - | insertion |
Pro 577 | - | insertion |
Arg 578 | - | insertion |
Gln 579 | - | insertion |
Gly 580 | - | insertion |
Gly 581 | - | insertion |
Arg 582 | - | insertion |
Tyr 583 | - | insertion |
Lys 584 | - | insertion |
PDB | External Database | Details |
---|---|---|
Ile 13 | Thr 13 | conflict |
Thr 139 | Pro 139 | conflict |
Asn 228 | Ser 228 | conflict |
Ile 259 | Met 259 | conflict |
PDB | External Database | Details |
---|---|---|
Arg 69 | Ile 69 | conflict |
PDB | External Database | Details |
---|---|---|
- | Gly 16 | deletion |
- | Thr 17 | deletion |
- | Phe 18 | deletion |
- | Arg 19 | deletion |
- | Lys 20 | deletion |
- | Phe 21 | deletion |
- | Arg 22 | deletion |
- | Arg 23 | deletion |
- | Asn 24 | deletion |
- | Asp 25 | deletion |
- | Tyr 26 | deletion |
- | Thr 27 | deletion |
- | Phe 28 | deletion |
- | Gly 29 | deletion |
- | Arg 30 | deletion |
- | Thr 31 | deletion |
- | Arg 32 | deletion |
- | Gly 33 | deletion |
- | Arg 34 | deletion |
- | Glu 35 | deletion |
- | Lys 36 | deletion |
- | Lys 37 | deletion |
- | Arg 38 | deletion |
- | Gly 39 | deletion |
- | Thr 40 | deletion |
- | Thr 41 | deletion |
- | Ser 42 | deletion |
- | Ser 43 | deletion |
- | Lys 44 | deletion |
- | Ile 45 | deletion |
- | Gly 46 | deletion |
- | Glu 47 | deletion |
- | Leu 48 | deletion |
- | Asp 49 | deletion |
- | Ile 50 | deletion |
- | Asn 51 | deletion |
- | Gly 52 | deletion |
PDB | External Database | Details |
---|---|---|
- | Ser 22 | deletion |
- | Lys 23 | deletion |
- | Ile 24 | deletion |
- | Leu 25 | deletion |
- | Thr 26 | deletion |
- | Ile 27 | deletion |
- | Ala 28 | deletion |
- | Phe 29 | deletion |
- | Pro 30 | deletion |
- | Pro 31 | deletion |
- | Pro 32 | deletion |
- | Leu 33 | deletion |
- | Thr 34 | deletion |
Sequence viewer
Contents of the asymmetric unit
Polymers | Number of chains | 60 |
Total formula weight | 3467344.1 | |
Non-Polymers* | Number of molecules | 5 |
Total formula weight | 1105.5 | |
All* | Total formula weight | 3468449.6 |