MolNFT v1 · #176725 · protein + RNA

Cryo-EM structure of the activated human minor spliceosome (minor bact complex)

7DVQ · Pre-mRNA-processing-splicing factor 8: “Cryo-EM structure of the activated human minor spliceosome (minor bact complex)”. Electron microscopy, 6 ligands (IHP, GTP, G5J), 20 pockets (best druggability 0.90). MolNFT v1 #176725 on…

PDB: 7DVQ
Type: protein + RNA
Length: 13,602 residues
Chains: 49
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA-processing-splicing factor 8; U5 snrna; 116 kda U5 small nuclear…
EC: 3.6.4.13, 2.3.2.27, 5.2.1.8
UniProt: Q6P2Q9, Q15029, O75643, Q96DI7, P62318, P14678, P62314, P62316, P62306, P62304, P62308, Q9BWG6, O75533, Q13435, Q15393, Q15427, Q9Y3B4, Q7RTV0, Q9BWJ5, Q99459, Q9BZJ0, Q9P013, Q13573, O43660, Q8TAD8, Q9Y388, Q9BRD0, Q13356, Q6UX04, O60231, Q92917, O15541, Q9UQ35, Q9HCG8, Q8IYB3, Q9P021, Q5RL73, Q9H6L4
Ligands: IHP, GTP, G5J, ZN, MG, K
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 46 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-processing-splicing factor 8	protein	2223	43% helix, 13% strand	Q6P2Q9
B	U5 snrna	rna	90	—	—
C	116 kda U5 small nuclear ribonucleoprotein component	protein	902	34% helix, 23% strand	Q15029
D	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1803	43% helix, 16% strand	O75643
E	U5 small nuclear ribonucleoprotein 40 kda protein	protein	299	0% helix, 48% strand	Q96DI7
a	Small nuclear ribonucleoprotein sm D3	protein	81	19% helix, 48% strand	P62318
b	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	82	4% helix, 49% strand	P14678
c, j	Small nuclear ribonucleoprotein sm D1	protein	82	16% helix, 45% strand	P62314
d	Small nuclear ribonucleoprotein sm D2	protein	97	19% helix, 45% strand	P62316
f, m	Small nuclear ribonucleoprotein F	protein	74	15% helix, 57% strand	P62306
e, l	Small nuclear ribonucleoprotein E	protein	79	18% helix, 58% strand	P62304
g	Small nuclear ribonucleoprotein G	protein	74	8% helix, 54% strand	P62308
F	U6ATAC snrna	rna	60	—	—
G	Pre-mRNA	rna	63	—	—
H	U12 snrna	rna	63	—	—
h	Small nuclear ribonucleoprotein sm D3	protein	80	13% helix, 49% strand	P62318
i	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	86	8% helix, 47% strand	P14678
k	Small nuclear ribonucleoprotein sm D2	protein	85	21% helix, 51% strand	P62316
n	Small nuclear ribonucleoprotein G	protein	68	9% helix, 56% strand	P62308
v	Sodium channel modifier 1	protein	119	40% helix, 8% strand	Q9BWG6
1	Splicing factor 3B subunit 1	protein	986	71% helix, 1% strand	O75533
2	Splicing factor 3B subunit 2	protein	216	34% helix, 1% strand	Q13435
3	Splicing factor 3B subunit 3	protein	1193	8% helix, 49% strand	Q15393
4	Splicing factor 3B subunit 4	protein	78	28% helix, 21% strand	Q15427
5	Splicing factor 3B subunit 6	protein	109	31% helix, 24% strand	Q9Y3B4
6	Phd finger-like domain-containing protein 5A	protein	105	28% helix, 19% strand	Q7RTV0
7	Splicing factor 3B subunit 5	protein	81	68% helix, 0% strand	Q9BWJ5
L	Cell division cycle 5-like protein	protein	101	66% helix, 0% strand	Q99459
J	Crooked neck-like protein 1	protein	522	75% helix, 0% strand	Q9BZJ0
P	Spliceosome-associated protein CWC15 homolog	protein	44	30% helix, 0% strand	Q9P013
R	Snw domain-containing protein 1	protein	241	40% helix, 1% strand	Q13573
T	Pleiotropic regulator 1	protein	320	1% helix, 50% strand	O43660
X	Smad nuclear-interacting protein 1	protein	156	3% helix, 35% strand	Q8TAD8
Y	RNA-binding motif protein, X-linked 2	protein	140	39% helix, 21% strand	Q9Y388
Z	BUD13 homolog	protein	140	58% helix, 0% strand	Q9BRD0
9	Ring-type E3 ubiquitin-protein ligase PPIL2 (EC 2.3.2.27)	protein	409	24% helix, 20% strand	Q13356
z	Peptidyl-prolyl cis-trans isomerase CWC27 homolog (EC 5.2.1.8)	protein	177	12% helix, 27% strand	Q6UX04
x	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.4.13)	protein	599	43% helix, 19% strand	O60231
y	G-patch domain and kow motifs-containing protein	protein	13	0% helix, 23% strand	Q92917
M	Ring finger protein 113A	protein	191	24% helix, 8% strand	O15541
U	SERINE/ARGININE repetitive matrix protein 2	protein	26	12% helix, 8% strand	Q9UQ35
V	Pre-mRNA-splicing factor CWC22 homolog	protein	468	72% helix, 1% strand	Q9HCG8
8	SERINE/ARGININE repetitive matrix protein 1	protein	126	49% helix, 0% strand	Q8IYB3
0	Cysteine-rich PDZ-binding protein	protein	100	11% helix, 5% strand	Q9P021
I	RNA-binding protein 48	protein	128	28% helix, 23% strand	Q5RL73
K	Armadillo repeat-containing protein 7	protein	188	72% helix, 0% strand	Q9H6L4

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A, M
GTP · Guanosine-5'-triphosphate · ligand · chains A, C
G5J · 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine · ligand · chains F, I, K
ZN · Zinc ion · metal · 7 copies · chains v, 6, M, 0
MG · Magnesium ion · metal · 5 copies · chains C, F, G, v, A
K · Potassium ion · metal · 2 copies · chains F

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	1128	0.90	0.92	151	empty
2	845	0.89	0.91	110	empty
3	953	0.86	0.88	122	empty
4	1083	0.86	0.87	104	empty
5	608	0.85	0.90	72	empty

Interfaces

159 interfaces between chains.

A–C · 5411 Å² buried · 53 hydrogen bonds · protein-protein
A–R · 5367 Å² buried · 48 hydrogen bonds · protein-protein
A–M · 3628 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 3119 Å² buried · 50 hydrogen bonds · protein-nucleic
A–1 · 3107 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified, 1 covalent (phosphorylation, covalent ligand).

Compared structures

7DVQ · Cryo-EM Structure of the Activated Human Minor Spliceosome (minor Bact Complex) · the same entry in another collection · chain e against e, 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 Q6P2Q9
Every structure of UniProt Q15029
Every structure of UniProt O75643
Every structure of UniProt Q96DI7
Every structure of UniProt P62318
Every structure of UniProt P14678
Every structure of UniProt P62314
Every structure of UniProt P62316
Every structure of UniProt P62306
Every structure of UniProt P62304
Every structure of UniProt P62308
Every structure of UniProt Q9BWG6
Every structure of UniProt O75533
Every structure of UniProt Q13435
Every structure of UniProt Q15393
Every structure of UniProt Q15427
Every structure of UniProt Q9Y3B4
Every structure of UniProt Q7RTV0
Every structure of UniProt Q9BWJ5
Every structure of UniProt Q99459
Every structure of UniProt Q9BZJ0
Every structure of UniProt Q9P013
Every structure of UniProt Q13573
Every structure of UniProt O43660
Every structure of UniProt Q8TAD8
Every structure of UniProt Q9Y388
Every structure of UniProt Q9BRD0
Every structure of UniProt Q13356
Every structure of UniProt Q6UX04
Every structure of UniProt O60231
Every structure of UniProt Q92917
Every structure of UniProt O15541
Every structure of UniProt Q9UQ35
Every structure of UniProt Q9HCG8
Every structure of UniProt Q8IYB3
Every structure of UniProt Q9P021
Every structure of UniProt Q5RL73
Every structure of UniProt Q9H6L4
Elsewhere: RCSB PDB 7DVQ · PDBe 7DVQ · UniProt Q6P2Q9 · UniProt Q15029 · UniProt O75643 · UniProt Q96DI7 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt Q9BWG6 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9Y3B4 · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q99459 · UniProt Q9BZJ0 · UniProt Q9P013 · UniProt Q13573 · UniProt O43660 · UniProt Q8TAD8 · UniProt Q9Y388 · UniProt Q9BRD0 · UniProt Q13356 · UniProt Q6UX04 · UniProt O60231 · UniProt Q92917 · UniProt O15541 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt Q8IYB3 · UniProt Q9P021 · UniProt Q5RL73 · UniProt Q9H6L4

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