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Core of mammalian 80S pre-ribosome in complex with trnas fitted to a 9.8A cryo-EM MAP: classic pre state 1

Analyse Core of mammalian 80S pre-ribosome in complex with trnas fitted to a 9.8A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J0L
Type: protein + RNA
Length: 1,968 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 40S ribosomal RNA fragment; Ribosomal protein S5; Ribosomal protein S14; Ribosomal…
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 30 distinct chains · 27% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	40S ribosomal RNA fragment	rna	48	—	—
b	40S ribosomal RNA fragment	rna	12	—	—
c	40S ribosomal RNA fragment	rna	17	—	—
d	40S ribosomal RNA fragment	rna	7	—	—
e	40S ribosomal RNA fragment	rna	4	—	—
E	40S ribosomal RNA fragment	rna	5	—	—
f	40S ribosomal RNA fragment	rna	21	—	—
g	40S ribosomal RNA fragment	rna	31	—	—
G	40S ribosomal RNA fragment	rna	13	—	—
h	40S ribosomal RNA fragment	rna	111	—	—
T	Ribosomal protein S5	protein	192	51% helix, 8% strand	—
K	Ribosomal protein S14	protein	140	26% helix, 21% strand	—
L	Ribosomal protein S23	protein	141	23% helix, 28% strand	—
X	Ribosomal protein S30	protein	68	34% helix, 0% strand	—
S	Ribosomal protein S15	protein	125	39% helix, 12% strand	—
1	60S ribosomal RNA fragment	rna	50	—	—
2	60S ribosomal RNA fragment	rna	112	—	—
3	60S ribosomal RNA fragment	rna	12	—	—
4	60S ribosomal RNA fragment	rna	14	—	—
5	60S ribosomal RNA fragment	rna	6	—	—
6	60S ribosomal RNA fragment	rna	19	—	—
7	60S ribosomal RNA fragment	rna	50	—	—
8	60S ribosomal RNA fragment	rna	20	—	—
B	Ribosomal protein L10A	protein	213	14% helix, 0% strand	—
J	Ribosomal protein L10	protein	208	24% helix, 12% strand	—
F	Ribosomal protein L36A	protein	95	6% helix, 11% strand	—
Y, V	TRNA	rna	75	—	—
y, v	MRNA fragment	rna	3	—	—
W	TRNA	rna	76	—	—
w	MRNA fragment	rna	2	—	—

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	765	0.79	0.84	123	empty
2	1016	0.78	0.80	148	empty
3	841	0.76	0.81	64	empty
4	880	0.73	0.78	63	empty
5	633	0.67	0.77	35	empty

Interfaces

69 interfaces between chains.

a–X · 1321 Å² buried · 29 hydrogen bonds · protein-nucleic
g–G · 774 Å² buried · 59 hydrogen bonds · nucleic-nucleic
1–J · 773 Å² buried · 45 hydrogen bonds · protein-nucleic
a–L · 722 Å² buried · 23 hydrogen bonds · protein-nucleic
h–2 · 702 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Compared structures

3J0L · Core of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9.8A cryo-EM map… · the same entry in another collection · chain b against b, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3J0L · PDBe 3J0L

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