MolNFT v1 · #152287 · protein + RNA

Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 ångström

6ICZ · Protein mago nashi homolog 2: “Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 ångström”. Electron microscopy, 5 ligands (IHP, GTP, ATP), 20 pockets (best druggability 0.89). MolNFT v1 #152287 on…

PDB: 6ICZ
Type: protein + RNA
Length: 14,593 residues
Chains: 51
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein mago nashi homolog 2; RNA-binding protein 8A; Eukaryotic initiation factor…
EC: 3.6.4.13, 5.2.1.8, 2.3.2.27
UniProt: Q96A72, Q9Y5S9, P38919, O15234, Q6P2Q9, Q15029, Q96DI7, Q9BZJ0, Q99459, O95926, P41223, Q9NW64, Q9P013, Q13573, Q9Y3C6, O43660, Q9UQ35, Q9HCG8, O60508, Q9H875, O95391, Q9HCS7, Q9UNP9, O60306, P62318, Q66K91, P62314, P62316, P62306, P62304, P62308, P09661, P08579, Q14562, O75934, Q9UMS4, O75643
Ligands: IHP, GTP, ATP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 47 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
v	Protein mago nashi homolog 2	protein	144	36% helix, 34% strand	Q96A72
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
A	Pre-mRNA-processing-splicing factor 8	protein	2253	42% helix, 12% strand	Q6P2Q9
B	U5SNRNA	rna	97	—	—
C	116 kda U5 small nuclear ribonucleoprotein component	protein	894	31% helix, 21% strand	Q15029
E	U5 small nuclear ribonucleoprotein 40 kda protein	protein	303	0% helix, 45% strand	Q96DI7
F	U6SNRNA	rna	97	—	—
G	Pre-mRNA	rna	84	—	—
H	U2SNRNA	rna	140	—	—
J	Crooked neck-like protein 1	protein	571	71% helix, 0% strand	Q9BZJ0
L	Cell division cycle 5-like protein	protein	454	68% helix, 1% strand	Q99459
M	Pre-mRNA-splicing factor SYF2	protein	130	56% helix, 0% strand	O95926
N	Protein BUD31 homolog	protein	143	45% helix, 0% strand	P41223
O	Pre-mRNA-splicing factor RBM22	protein	285	28% helix, 18% strand	Q9NW64
P	Spliceosome-associated protein CWC15 homolog	protein	110	34% helix, 1% strand	Q9P013
R	Snw domain-containing protein 1	protein	261	28% helix, 7% strand	Q13573
S	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8)	protein	159	15% helix, 28% strand	Q9Y3C6
T	Pleiotropic regulator 1	protein	313	0% helix, 52% strand	O43660
U	SERINE/ARGININE repetitive matrix protein 2	protein	26	0% helix, 12% strand	Q9UQ35
V	Pre-mRNA-splicing factor CWC22 homolog	protein	452	73% helix, 0% strand	Q9HCG8
W	Pre-mRNA-processing factor 17	protein	508	9% helix, 31% strand	O60508
X	Prkr-interacting protein 1	protein	92	70% helix, 0% strand	Q9H875
Z	Pre-mRNA-splicing factor SLU7	protein	242	29% helix, 2% strand	O95391
I	Pre-mRNA-splicing factor SYF1	protein	564	80% helix, 0% strand	Q9HCS7
y	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	79	28% helix, 35% strand	Q9UNP9
Q	RNA helicase aquarius (EC 3.6.4.13)	protein	1322	49% helix, 12% strand	O60306
h, a	Small nuclear ribonucleoprotein sm D3	protein	81	14% helix, 48% strand	P62318
i, b	Small nuclear ribonucleoprotein-associated protein	protein	86	8% helix, 47% strand	Q66K91
j, c	Small nuclear ribonucleoprotein sm D1	protein	82	16% helix, 45% strand	P62314
k	Small nuclear ribonucleoprotein sm D2	protein	85	21% helix, 51% strand	P62316
m	Small nuclear ribonucleoprotein F	protein	73	15% helix, 58% strand	P62306
l, e	Small nuclear ribonucleoprotein E	protein	79	18% helix, 56% strand	P62304
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
Y	ATP-dependent RNA helicase DHX8 (EC 3.6.4.13)	protein	713	41% helix, 16% strand	Q14562
d	Small nuclear ribonucleoprotein sm D2	protein	97	19% helix, 46% strand	P62316
f	Small nuclear ribonucleoprotein F	protein	74	15% helix, 57% strand	P62306
g	Small nuclear ribonucleoprotein G	protein	74	8% helix, 54% strand	P62308
K	Pre-mRNA-splicing factor SPF27	protein	152	76% helix, 0% strand	O75934
q	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	132	55% helix, 7% strand	Q9UMS4
r	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	131	55% helix, 8% strand	Q9UMS4
s	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	67	93% helix, 0% strand	Q9UMS4
t	Pre-mRNA-processing factor 19 (EC 2.3.2.27)	protein	67	93% helix, 0% strand	Q9UMS4
D	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1722	41% helix, 18% strand	O75643

Ligands and binding sites

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

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	1119	0.89	0.91	139	MG
2	1096	0.89	0.90	102	empty
3	1041	0.86	0.87	75	empty
4	1000	0.85	0.87	133	empty
5	639	0.85	0.89	89	empty

Interfaces

160 interfaces between chains.

A–Z · 6166 Å² buried · 59 hydrogen bonds · protein-protein
A–C · 6101 Å² buried · 56 hydrogen bonds · protein-protein
J–L · 3336 Å² buried · 45 hydrogen bonds · protein-protein
A–B · 3276 Å² buried · 62 hydrogen bonds · protein-nucleic
A–G · 2652 Å² buried · 42 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

6ICZ · Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom · the same entry in another collection · chain H against H, 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 Q96A72
Every structure of UniProt Q9Y5S9
Every structure of UniProt P38919
Every structure of UniProt O15234
Every structure of UniProt Q6P2Q9
Every structure of UniProt Q15029
Every structure of UniProt Q96DI7
Every structure of UniProt Q9BZJ0
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 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 Q9H875
Every structure of UniProt O95391
Every structure of UniProt Q9HCS7
Every structure of UniProt Q9UNP9
Every structure of UniProt O60306
Every structure of UniProt P62318
Every structure of UniProt Q66K91
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 P09661
Every structure of UniProt P08579
Every structure of UniProt Q14562
Every structure of UniProt O75934
Every structure of UniProt Q9UMS4
Every structure of UniProt O75643
Elsewhere: RCSB PDB 6ICZ · PDBe 6ICZ · UniProt Q96A72 · UniProt Q9Y5S9 · UniProt P38919 · UniProt O15234 · UniProt Q6P2Q9 · UniProt Q15029 · UniProt Q96DI7 · UniProt Q9BZJ0 · UniProt Q99459 · UniProt O95926 · UniProt P41223 · UniProt Q9NW64 · UniProt Q9P013 · UniProt Q13573 · UniProt Q9Y3C6 · UniProt O43660 · UniProt Q9UQ35 · UniProt Q9HCG8 · UniProt O60508 · UniProt Q9H875 · UniProt O95391 · UniProt Q9HCS7 · UniProt Q9UNP9 · UniProt O60306 · UniProt P62318 · UniProt Q66K91 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P09661 · UniProt P08579 · UniProt Q14562 · UniProt O75934 · UniProt Q9UMS4 · UniProt O75643

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