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The cryo-EM structure of human pre-C*-II complex

Analyse The cryo-EM structure of human pre-C*-II complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7W5A
Type: protein + RNA
Length: 13,049 residues
Chains: 54
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, 5.2.1.8, 2.3.2.27
UniProt: Q6P2Q9, Q15029, Q96DI7, Q9HCS7, Q9BZJ0, O75934, Q99459, O95926, P41223, Q9NW64, Q9P013, O60306, Q13573, Q9Y3C6, O43660, Q9UQ35, Q9HCG8, O60508, Q9GZU8, Q14562, Q8WUQ7, Q9H875, Q9Y421, P14678, Q9UNP9, P62318, P62314, P62316, P62306, P62304, P62308, P61326, Q9Y5S9, P38919, O15234, Q9UMS4, P09661, P08579, O95391
Ligands: IHP, GTP, ATP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 49 distinct chains · 41% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-processing-splicing factor 8	protein	1984	43% helix, 9% strand	Q6P2Q9
B	U5 snrna	rna	84	—	—
C	116 kda U5 small nuclear ribonucleoprotein component	protein	862	34% helix, 23% strand	Q15029
E	U5 small nuclear ribonucleoprotein 40 kda protein	protein	299	0% helix, 48% strand	Q96DI7
F	U6 snrna	rna	97	—	—
4	Pre-mRNA	rna	13	—	—
G	Pre-mRNA	rna	82	—	—
H	U2 snrna	rna	140	—	—
I	Pre-mRNA-splicing factor SYF1	protein	618	78% helix, 0% strand	Q9HCS7
J	Crooked neck-like protein 1	protein	567	69% helix, 1% strand	Q9BZJ0
K	Pre-mRNA-splicing factor SPF27	protein	155	78% helix, 0% strand	O75934
L	Cell division cycle 5-like protein	protein	437	68% helix, 1% strand	Q99459
M	Pre-mRNA-splicing factor SYF2	protein	130	53% helix, 0% strand	O95926
N	Protein BUD31 homolog	protein	143	43% helix, 0% strand	P41223
O	Pre-mRNA-splicing factor RBM22	protein	285	26% helix, 18% strand	Q9NW64
P	Spliceosome-associated protein CWC15 homolog	protein	113	32% helix, 1% strand	Q9P013
Q	RNA helicase aquarius (EC 3.6.4.13)	protein	1322	50% helix, 12% strand	O60306
R	Snw domain-containing protein 1	protein	261	28% helix, 6% strand	Q13573
S	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8)	protein	159	14% helix, 31% strand	Q9Y3C6
T	Pleiotropic regulator 1	protein	312	1% helix, 49% strand	O43660
U	SERINE/ARGININE repetitive matrix protein 2	protein	72	56% helix, 1% strand	Q9UQ35
V	Pre-mRNA-splicing factor CWC22 homolog	protein	452	68% helix, 0% strand	Q9HCG8
W	Pre-mRNA-processing factor 17	protein	509	7% helix, 28% strand	O60508
X	PSME3-interacting protein	protein	87	87% helix, 0% strand	Q9GZU8
Y	ATP-dependent RNA helicase DHX8 (EC 3.6.4.13)	protein	667	42% helix, 18% strand	Q14562
Z	Cactin	protein	101	0% helix, 42% strand	Q8WUQ7
2	Prkr-interacting protein 1	protein	123	59% helix, 0% strand	Q9H875
z	Protein FAM32A	protein	60	60% helix, 0% strand	Q9Y421
b	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	102	7% helix, 42% strand	P14678
y	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	79	28% helix, 34% strand	Q9UNP9
a	Small nuclear ribonucleoprotein sm D3	protein	77	14% helix, 51% strand	P62318
c, j	Small nuclear ribonucleoprotein sm D1	protein	82	16% helix, 45% strand	P62314
d	Small nuclear ribonucleoprotein sm D2	protein	97	19% helix, 46% 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
v	Protein mago nashi homolog	protein	144	36% helix, 34% strand	P61326
w	RNA-binding protein 8A	protein	91	24% helix, 35% strand	Q9Y5S9
u	Eukaryotic initiation factor 4A-III (EC 3.6.4.13)	protein	386	41% helix, 17% strand	P38919
x	Protein CASC3	protein	25	12% helix, 0% strand	O15234
q, s	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	132	55% helix, 5% strand	Q9UMS4
r, t	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	131	55% helix, 8% strand	Q9UMS4
h	Small nuclear ribonucleoprotein sm D3	protein	81	14% helix, 48% 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	69	9% helix, 55% strand	P62308
o	U2 small nuclear ribonucleoprotein a'	protein	162	27% helix, 17% strand	P09661
p	U2 small nuclear ribonucleoprotein B''	protein	94	32% helix, 24% strand	P08579
1	Pre-mRNA-splicing factor SLU7	protein	267	29% helix, 1% strand	O95391

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A, 1
GTP · Guanosine-5'-triphosphate · ligand · chains A, C
ATP · Adenosine-5'-triphosphate · ligand · chains Q
MG · Magnesium ion · metal · 9 copies · chains C, F, 4, G, A, Q
ZN · Zinc ion · metal · 7 copies · chains N, O, 1

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	1092	0.89	0.91	113	MG
2	673	0.88	0.93	91	empty
3	811	0.88	0.91	89	MG
4	774	0.88	0.91	91	empty
5	1178	0.87	0.88	125	empty

Interfaces

189 interfaces between chains.

A–C · 6250 Å² buried · 61 hydrogen bonds · protein-protein
A–1 · 6175 Å² buried · 81 hydrogen bonds · protein-protein
J–L · 3206 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 3158 Å² buried · 64 hydrogen bonds · protein-nucleic
A–R · 2704 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

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

Compared structures

7W5A · The cryo-EM structure of human pre-C*-II complex · the same entry in another collection · chain 4 against 4, 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 Q96DI7
Every structure of UniProt Q9HCS7
Every structure of UniProt Q9BZJ0
Every structure of UniProt O75934
Every structure of UniProt Q99459
Every structure of UniProt O95926
Every structure of UniProt P41223
Every structure of UniProt Q9NW64
Every structure of UniProt Q9P013
Every structure of UniProt O60306
Every structure of UniProt Q13573
Every structure of UniProt Q9Y3C6
Every structure of UniProt O43660
Every structure of UniProt Q9UQ35
Every structure of UniProt Q9HCG8
Every structure of UniProt O60508
Every structure of UniProt Q9GZU8
Every structure of UniProt Q14562
Every structure of UniProt Q8WUQ7
Every structure of UniProt Q9H875
Every structure of UniProt Q9Y421
Every structure of UniProt P14678
Every structure of UniProt Q9UNP9
Every structure of UniProt P62318
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 P61326
Every structure of UniProt Q9Y5S9
Every structure of UniProt P38919
Every structure of UniProt O15234
Every structure of UniProt Q9UMS4
Every structure of UniProt P09661
Every structure of UniProt P08579
Every structure of UniProt O95391
Elsewhere: RCSB PDB 7W5A · PDBe 7W5A · UniProt Q6P2Q9 · UniProt Q15029 · UniProt Q96DI7 · UniProt Q9HCS7 · UniProt Q9BZJ0 · UniProt O75934 · UniProt Q99459 · UniProt O95926 · UniProt P41223 · UniProt Q9NW64 · UniProt Q9P013 · UniProt O60306 · UniProt Q13573 · UniProt Q9Y3C6 · UniProt O43660 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt O60508 · UniProt Q9GZU8 · UniProt Q14562 · UniProt Q8WUQ7 · UniProt Q9H875 · UniProt Q9Y421 · UniProt P14678 · UniProt Q9UNP9 · UniProt P62318 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P61326 · UniProt Q9Y5S9 · UniProt P38919 · UniProt O15234 · UniProt Q9UMS4 · UniProt P09661 · UniProt P08579 · UniProt O95391

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