Research workbench

The overall structure of the yeast spliceosomal U4/U6.U5 tri-snrnp at 3.7 ångström

Analyse The overall structure of the yeast spliceosomal U4/U6.U5 tri-snrnp at 3.7… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GAN
Type: protein + RNA
Length: 9,325 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U4 snrna; U6 snrna; Pre-mRNA-splicing factor 8; U4/U6 small nuclear ribonucleoprotein…
EC: 3.6.4.13
UniProt: P33334, P20053, P19735, Q06819, P49704, Q03338, P32639, P40018, Q02260, Q06217, P43321, Q12330, P54999, P40204, P39990, P38203, P57743, P40070, P40089, A6ZYX7, P53905, P47093, P36048
Ligands: GTP
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 29 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V	U4 snrna	rna	124	—	—
W	U6 snrna	rna	80	—	—
A	Pre-mRNA-splicing factor 8	protein	2196	45% helix, 12% strand	P33334
H	U4/U6 small nuclear ribonucleoprotein PRP4	protein	357	13% helix, 40% strand	P20053
J	Pre-mRNA-splicing factor 6	protein	729	72% helix, 1% strand	P19735
D	Spliceosomal protein DIB1	protein	140	31% helix, 23% strand	Q06819
F	Pre-mRNA-processing factor 31	protein	415	58% helix, 2% strand	P49704
G	U4/U6 small nuclear ribonucleoprotein PRP3	protein	318	41% helix, 12% strand	Q03338
B	Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13)	protein	1781	43% helix, 14% strand	P32639
x	Unknown protein	protein	100	66% helix, 1% strand	—
k, b	Small nuclear ribonucleoprotein-associated protein B	protein	80	0% helix, 35% strand	P40018
l	Small nuclear ribonucleoprotein sm D1	protein	91	18% helix, 18% strand	Q02260
m, j	Small nuclear ribonucleoprotein sm D2	protein	94	20% helix, 37% strand	Q06217
n, d	Small nuclear ribonucleoprotein sm D3	protein	82	10% helix, 44% strand	P43321
p, e	Small nuclear ribonucleoprotein E	protein	75	15% helix, 32% strand	Q12330
q, f	Small nuclear ribonucleoprotein F	protein	72	10% helix, 53% strand	P54999
r, g	Small nuclear ribonucleoprotein G	protein	69	0% helix, 38% strand	P40204
E	SNU66	protein	328	39% helix, 0% strand	—
h	Small nuclear ribonucleoprotein sm D1	protein	82	15% helix, 46% strand	Q02260
U	U5 snrna	rna	141	—	—
K	13 kda ribonucleoprotein-associated protein	protein	124	48% helix, 16% strand	P39990
2	U6 snrna-associated sm-like protein LSM2	protein	90	19% helix, 30% strand	P38203
3	U6 snrna-associated sm-like protein LSM3	protein	77	5% helix, 51% strand	P57743
4	U6 snrna-associated sm-like protein LSM4	protein	74	16% helix, 49% strand	P40070
5	U6 snrna-associated sm-like protein LSM5	protein	75	9% helix, 55% strand	P40089
6	U6 snrna-associated sm-like protein LSM6	protein	74	9% helix, 58% strand	A6ZYX7
7	U6 snrna-associated sm-like protein LSM7	protein	66	0% helix, 52% strand	P53905
8	U6 snrna-associated sm-like protein LSM8	protein	64	0% helix, 53% strand	P47093
C	Pre-mRNA-splicing factor SNU114	protein	855	38% helix, 20% strand	P36048

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains A, C

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	1014	0.88	0.89	111	empty
2	1051	0.86	0.88	90	GTP
3	811	0.85	0.88	85	empty
4	1006	0.84	0.85	92	empty
5	680	0.84	0.88	65	empty

Interfaces

94 interfaces between chains.

A–C · 4798 Å² buried · 47 hydrogen bonds · protein-protein
A–F · 4144 Å² buried · 36 hydrogen bonds · protein-protein
A–U · 3458 Å² buried · 61 hydrogen bonds · protein-nucleic
V–B · 3396 Å² buried · 47 hydrogen bonds · protein-nucleic
A–J · 3063 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5GAN · The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom · the same entry in another collection · chain k against k, 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 P19735
Every structure of UniProt Q06819
Every structure of UniProt P49704
Every structure of UniProt Q03338
Every structure of UniProt P32639
Every structure of UniProt P40018
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt P43321
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Every structure of UniProt P39990
Every structure of UniProt P38203
Every structure of UniProt P57743
Every structure of UniProt P40070
Every structure of UniProt P40089
Every structure of UniProt A6ZYX7
Every structure of UniProt P53905
Every structure of UniProt P47093
Every structure of UniProt P36048
Elsewhere: RCSB PDB 5GAN · PDBe 5GAN · UniProt P33334 · UniProt P20053 · UniProt P19735 · UniProt Q06819 · UniProt P49704 · UniProt Q03338 · UniProt P32639 · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt P43321 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P39990 · UniProt P38203 · UniProt P57743 · UniProt P40070 · UniProt P40089 · UniProt A6ZYX7 · UniProt P53905 · UniProt P47093 · UniProt P36048

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