MolNFT v2 · #217160 · protein + RNA

Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure

8PVL · 26S rRNA: “Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure”. Electron microscopy at 2.19, 3 ligands (GTP, ZN, MG), 20 pockets (best druggability 0.89). MolNFT v2 #217160 on…

PDB: 8PVL
Type: protein + RNA
Length: 13,518 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.19
Source: Thermochaetoides thermophila DSM 1495
Molecule: 26S rRNA; 5.8S rRNA; ITS2; 5S rRNA; Large ribosomal subunit protein uL10; Nucleolar…
EC: 2.4.99.18
UniProt: G0S616, G0S8F1, G0S1H0, G0SHX6, G0S081, G0SEW3, G0SFL0, G0S683, G0SHK0, G0S497, G0SB32, G0SBX1, G0S495, G0SF80, G0SCH6, G0SC29, G0SCP3, G0S4P8, G0RXW1, G0SFC3, G0SEG2, G0S0D6, G0SAJ9, G0SHQ2, G0SGH8, G0S992, G0S1R0, G0RZ88, G0SH61, G0SGY1, G0S9B5, G0S9T3, G0SCE2, G0S0Z3, G0SDS8, G0SI44, G0S507, G0RYN9, G0RZE9, G0SEI0, G0SD68, G0S6V4, G0SCL3, G0SFN0, G0S0D7, G0SBN1, G0S101, Q2H9R2, G0S6B0, G0SHJ6
Ligands: GTP, ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.19 · 58 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C1	26S rRNA	rna	3078	—	—
C2	5.8S rRNA	rna	156	—	—
C3	ITS2	rna	3	—	—
C4	5S rRNA	rna	119	—	—
CF	Large ribosomal subunit protein uL10	protein	245	28% helix, 21% strand	G0S616
CH	Nucleolar GTP-binding protein 1	protein	627	52% helix, 8% strand	G0S8F1
CI	Putative RNA-binding protein	protein	91	21% helix, 35% strand	G0S1H0
CJ	Pescadillo homolog	protein	382	46% helix, 13% strand	G0SHX6
CK	Ribosome biogenesis protein NSA2 homolog	protein	237	34% helix, 24% strand	G0S081
CL	Putative GTP binding protein	protein	79	52% helix, 0% strand	G0SEW3
CM	60S ribosomal protein l7-like protein	protein	216	57% helix, 13% strand	G0SFL0
CN	Eukaryotic translation initiation factor 6	protein	246	34% helix, 24% strand	G0S683
CO	DUF2423 domain-containing protein	protein	62	63% helix, 0% strand	G0SHK0
CQ	Ribosome biogenesis protein RLP24	protein	183	51% helix, 9% strand	G0S497
Cb	Zinc finger domain-containing protein	protein	101	55% helix, 8% strand	G0SB32
Cd	Nucleolar GTP-binding protein 2	protein	462	44% helix, 12% strand	G0SBX1
Ce	Ribosome biogenesis protein NOP53	protein	239	54% helix, 4% strand	G0S495
Cf	Ribosome production factor 2 homolog	protein	285	22% helix, 31% strand	G0SF80
Cg	Ribosome biogenesis regulatory protein	protein	188	39% helix, 14% strand	G0SCH6
Ch	Ribosome assembly protein 4	protein	485	10% helix, 44% strand	G0SC29
Cz	rRNA-processing protein	protein	101	70% helix, 0% strand	G0SCP3
LA	60S ribosomal protein L2-like protein	protein	191	12% helix, 32% strand	G0S4P8
LB	60S ribosomal protein L3-like protein	protein	389	17% helix, 28% strand	G0RXW1
LC	60S ribosomal protein L4-like protein	protein	363	33% helix, 10% strand	G0SFC3
LD	60S ribosomal protein l5-like protein	protein	286	47% helix, 12% strand	G0SEG2
LE	60S ribosomal protein L6	protein	191	25% helix, 20% strand	G0S0D6
LF	60S ribosomal protein l7-like protein	protein	248	56% helix, 15% strand	G0SFL0
LG	60S ribosomal protein L8	protein	235	51% helix, 8% strand	G0SAJ9
LH	60S ribosomal protein l9-like protein	protein	190	21% helix, 44% strand	—
LJ	Putative ribosomal protein	protein	169	31% helix, 23% strand	G0SHQ2
LK	60S ribosomal protein L12-like protein	protein	158	42% helix, 18% strand	G0SGH8
LL	60S ribosomal protein L13	protein	203	45% helix, 12% strand	G0S992
LM	60S ribosomal protein L14-like protein	protein	141	44% helix, 28% strand	G0S1R0
LN	Ribosomal protein L15	protein	202	42% helix, 18% strand	G0RZ88
LO	60S ribosomal protein L16-like protein	protein	203	55% helix, 11% strand	G0SH61
LP	60S ribosomal protein l17-like protein	protein	171	39% helix, 25% strand	G0SGY1
LQ	Ribosomal protein L18-like protein	protein	150	37% helix, 15% strand	G0S9B5
LR	Ribosomal protein L19	protein	155	65% helix, 4% strand	G0S9T3
LS	60S ribosomal protein L20	protein	174	24% helix, 32% strand	G0SCE2
LT	60S ribosomal protein l21-like protein	protein	129	26% helix, 30% strand	G0S0Z3
LU	60S ribosomal protein L22-like protein	protein	105	29% helix, 34% strand	G0SDS8
LV	60S ribosomal protein l23-like protein	protein	135	11% helix, 35% strand	G0SI44
LX	60S ribosomal protein L25-like protein	protein	145	34% helix, 21% strand	G0S507
LY	60S ribosomal protein L26-like protein	protein	133	35% helix, 26% strand	G0RYN9
LZ	60S ribosomal protein L27	protein	135	32% helix, 27% strand	G0RZE9
La	60S ribosomal protein L28-like protein	protein	108	38% helix, 20% strand	—
Lc	60S ribosomal protein l30-like protein	protein	95	45% helix, 20% strand	G0SEI0
Ld	Putative 60S ribosomal protein	protein	110	28% helix, 29% strand	G0SD68
Le	60S ribosomal protein L32-like protein	protein	126	22% helix, 10% strand	G0S6V4
Lf	60S ribosomal protein l33-like protein	protein	108	9% helix, 52% strand	G0SCL3
Lg	Ribosomal protein l34-like protein	protein	118	38% helix, 12% strand	G0SFN0
Lh	dolichyl-diphosphooligosaccharide--protein glycotransferase (EC 2.4.99.18)	protein	122	62% helix, 3% strand	G0S0D7
Li	60S ribosomal protein L36	protein	101	62% helix, 1% strand	G0SBN1
Lj	Ribosomal protein L37	protein	88	23% helix, 6% strand	G0S101
Lk	60S ribosomal protein L38-like protein	protein	76	22% helix, 36% strand	—
Ll	Ribosomal protein eL39	protein	50	36% helix, 0% strand	Q2H9R2
Lp	60S ribosomal protein L43-like protein	protein	91	43% helix, 14% strand	G0S6B0
Lq	Putative 60S ribosomal protein	protein	139	34% helix, 17% strand	G0SHJ6

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains CH, C1, Cd, Cf
ZN · Zinc ion · metal · 5 copies · chains CQ, Cb, Lg, Lj, Lp
MG · Magnesium ion · metal · 3 copies · chains CH, Cd

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	997	0.89	0.92	104	empty
2	982	0.89	0.91	113	empty
3	1104	0.88	0.90	112	empty
4	1122	0.87	0.89	98	empty
5	597	0.87	0.93	83	empty

Interfaces

219 interfaces between chains.

C1–LB · 8978 Å² buried · 211 hydrogen bonds · protein-nucleic
C1–LC · 8565 Å² buried · 201 hydrogen bonds · protein-nucleic
C1–LN · 7338 Å² buried · 149 hydrogen bonds · protein-nucleic
C1–CH · 7036 Å² buried · 183 hydrogen bonds · protein-nucleic
C1–Cd · 6860 Å² buried · 118 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 34 modified (nucleotide modification).

Compared structures

G0SC29 · AlphaFold monomer V2.0 prediction for ribosome assembly protein 4 (G0SC29) · a predicted model of the same protein · chain Ch against A, TM-score 0.96
G0S8F1 · AlphaFold monomer V2.0 prediction for nucleolar GTP-binding protein 1 (G0S8F1) · a predicted model of the same protein · chain CH against A, TM-score 0.79

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