MolNFT v1 · #68216 · protein + RNA

Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snrnp

3JCM · Pre-mRNA-splicing factor 8: “Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snrnp”. Electron microscopy, 2 ligands (GTP, M7M), 20 pockets (best druggability 0.85). MolNFT v1 #68216 on GenesisL1: 3D structure, binding sites and…

PDB: 3JCM
Type: protein + RNA
Length: 8,678 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA-splicing factor 8; U4/U6 small nuclear ribonucleoprotein PRP4…
EC: 3.6.4.13
UniProt: P33334, P20053, P49704, P19735, Q03338, Q06819, P39990, P36048, P32639, P43321, P40018, Q02260, Q06217, Q12330, P54999, P40204, P47093, P38203, P57743, Q06406, P40089, P53905, P40070
Ligands: GTP, M7M
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 29 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-splicing factor 8	protein	2174	43% helix, 13% strand	P33334
B	U4/U6 small nuclear ribonucleoprotein PRP4	protein	429	23% helix, 32% strand	P20053
I	Pre-mRNA-processing factor 31	protein	416	64% helix, 2% strand	P49704
G	Pre-mRNA-splicing factor 6	protein	734	70% helix, 0% strand	P19735
K	U4/U6 small nuclear ribonucleoprotein PRP3	protein	279	43% helix, 15% strand	Q03338
L	Spliceosomal protein DIB1	protein	139	30% helix, 19% strand	Q06819
M	13 kda ribonucleoprotein-associated protein	protein	126	46% helix, 14% strand	P39990
H	Pre-mRNA-splicing factor SNU114	protein	843	39% helix, 23% strand	P36048
N	Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13)	protein	1686	45% helix, 17% strand	P32639
R, J	Small nuclear ribonucleoprotein sm D3	protein	79	19% helix, 49% strand	P43321
S, O	Small nuclear ribonucleoprotein-associated protein B	protein	73	7% helix, 47% strand	P40018
T, P	Small nuclear ribonucleoprotein sm D1	protein	77	10% helix, 44% strand	Q02260
U	Small nuclear ribonucleoprotein sm D2	protein	90	20% helix, 39% strand	Q06217
V, Y	Small nuclear ribonucleoprotein E	protein	72	14% helix, 39% strand	Q12330
W, Z	Small nuclear ribonucleoprotein F	protein	70	11% helix, 59% strand	P54999
X	Small nuclear ribonucleoprotein G	protein	70	4% helix, 44% strand	P40204
Q	Small nuclear ribonucleoprotein sm D2	protein	89	20% helix, 39% strand	Q06217
a	Small nuclear ribonucleoprotein G	protein	71	4% helix, 44% strand	P40204
b	U6 snrna-associated sm-like protein LSM8	protein	65	9% helix, 58% strand	P47093
c	U6 snrna-associated sm-like protein LSM2	protein	92	25% helix, 36% strand	P38203
d	U6 snrna-associated sm-like protein LSM3	protein	77	4% helix, 64% strand	P57743
e	U6 snrna-associated sm-like protein LSM6	protein	74	14% helix, 50% strand	Q06406
f	U6 snrna-associated sm-like protein LSM5	protein	77	13% helix, 49% strand	P40089
g	U6 snrna-associated sm-like protein LSM7	protein	66	6% helix, 53% strand	P53905
h	U6 snrna-associated sm-like protein LSM4	protein	77	18% helix, 49% strand	P40070
C	Pre-mRNA	rna	20	—	—
D	SNR6 snrna	rna	44	—	—
E	SNR14 snrna	rna	85	—	—
F	SNR7-L snrna	rna	113	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, H
M7M · N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate) · ligand · chains K, D, E

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	1112	0.85	0.86	106	empty
2	1190	0.85	0.86	137	empty
3	621	0.85	0.90	57	empty
4	823	0.84	0.87	94	GTP
5	933	0.83	0.85	83	empty

Interfaces

78 interfaces between chains.

A–H · 5134 Å² buried · 41 hydrogen bonds · protein-protein
A–G · 3960 Å² buried · 22 hydrogen bonds · protein-protein
A–I · 3934 Å² buried · 38 hydrogen bonds · protein-protein
B–K · 3140 Å² buried · 20 hydrogen bonds · protein-protein
A–F · 3121 Å² buried · 49 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

3JCM · Cryo-EM structure of the spliceosomal U4/U6.U5 tri-snRNP · the same entry in another collection · chain S against S, 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
Every structure of UniProt P33334
Every structure of UniProt P20053
Every structure of UniProt P49704
Every structure of UniProt P19735
Every structure of UniProt Q03338
Every structure of UniProt Q06819
Every structure of UniProt P39990
Every structure of UniProt P36048
Every structure of UniProt P32639
Every structure of UniProt P43321
Every structure of UniProt P40018
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Every structure of UniProt P47093
Every structure of UniProt P38203
Every structure of UniProt P57743
Every structure of UniProt Q06406
Every structure of UniProt P40089
Every structure of UniProt P53905
Every structure of UniProt P40070
Elsewhere: RCSB PDB 3JCM · PDBe 3JCM · UniProt P33334 · UniProt P20053 · UniProt P49704 · UniProt P19735 · UniProt Q03338 · UniProt Q06819 · UniProt P39990 · UniProt P36048 · UniProt P32639 · UniProt P43321 · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P47093 · UniProt P38203 · UniProt P57743 · UniProt Q06406 · UniProt P40089 · UniProt P53905 · UniProt P40070

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