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Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution

Analyse Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ID0
Type: protein + RNA
Length: 10,794 residues
Chains: 42
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.9
Source: Homo sapiens
Molecule: Pre-mRNA-processing-splicing factor 8; U5snRNA; 116 kDa U5 small nuclear…
EC: 5.2.1.8, 2.3.2.27, 3.6.4.13
UniProt: Q6P2Q9, Q15029, Q96DI7, Q9BZJ0, Q99459, O95926, P41223, Q9NW64, Q9P013, Q13573, Q9Y3C6, O43660, O60508, Q2TBE0, Q9HCS7, P62318, Q66K91, P62314, P62316, P62306, P62304, P62308, Q9UMS4, O75934, P09661, P08579, O60306, Q9UNP9
Ligands: IHP, GTP, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 2.9 · 37 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-processing-splicing factor 8	protein	1981	43% helix, 10% strand	Q6P2Q9
B	U5snRNA	rna	98	—	—
C	116 kDa U5 small nuclear ribonucleoprotein component	protein	888	33% helix, 21% strand	Q15029
E	U5 small nuclear ribonucleoprotein 40 kDa protein	protein	303	0% helix, 50% strand	Q96DI7
F	U6snRNA	rna	97	—	—
J	Crooked neck-like protein 1	protein	556	71% helix, 0% strand	Q9BZJ0
L	Cell division cycle 5-like protein	protein	475	67% helix, 1% strand	Q99459
M	Pre-mRNA-splicing factor SYF2	protein	130	55% helix, 0% strand	O95926
N	Protein BUD31 homolog	protein	143	47% helix, 0% strand	P41223
O	Pre-mRNA-splicing factor RBM22	protein	290	28% helix, 15% strand	Q9NW64
P	Spliceosome-associated protein CWC15 homolog	protein	118	37% helix, 1% strand	Q9P013
R	SNW domain-containing protein 1	protein	272	27% helix, 6% strand	Q13573
S	Peptidyl-prolyl cis-trans isomerase-like 1 (EC 5.2.1.8)	protein	159	17% helix, 23% strand	Q9Y3C6
T	Pleiotropic regulator 1	protein	317	1% helix, 51% strand	O43660
W	Pre-mRNA-processing factor 17	protein	509	8% helix, 29% strand	O60508
G	pre-mRNA	rna	70	—	—
H	U2snRNA	rna	140	—	—
U	CWF19-like protein 2	protein	347	29% helix, 12% strand	Q2TBE0
I	Pre-mRNA-splicing factor SYF1	protein	568	77% helix, 0% strand	Q9HCS7
a, h	Small nuclear ribonucleoprotein Sm D3	protein	81	14% helix, 48% strand	P62318
b, i	Small nuclear ribonucleoprotein-associated protein	protein	86	8% helix, 47% strand	Q66K91
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
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
K	Pre-mRNA-splicing factor SPF27	protein	152	76% helix, 0% strand	O75934
k	Small nuclear ribonucleoprotein Sm D2	protein	85	21% helix, 51% strand	P62316
n	Small nuclear ribonucleoprotein G	protein	67	9% helix, 57% 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
Q	RNA helicase aquarius (EC 3.6.4.13)	protein	1322	49% helix, 12% strand	O60306
y	Peptidyl-prolyl cis-trans isomerase E (EC 5.2.1.8)	protein	79	28% helix, 35% strand	Q9UNP9

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A
GTP · Guanosine-5'-triphosphate · ligand · chains A, C
MG · Magnesium ion · metal · 7 copies · chains C, F, U, A
ZN · Zinc ion · metal · 7 copies · chains N, O, U

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	985	0.89	0.91	106	empty
2	721	0.88	0.92	90	MG
3	861	0.87	0.90	109	empty
4	914	0.87	0.89	108	empty
5	647	0.86	0.91	57	empty

Interfaces

138 interfaces between chains.

A–C · 5995 Å² buried · 58 hydrogen bonds · protein-protein
A–U · 5894 Å² buried · 52 hydrogen bonds · protein-protein
J–L · 3288 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 3214 Å² buried · 62 hydrogen bonds · protein-nucleic
A–R · 2733 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

6ID0 · Cryo-EM structure of a human intron lariat spliceosome prior to PRP43 loaded (ILS1… · the same entry in another collection · chain L against L, 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 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 O60508
Every structure of UniProt Q2TBE0
Every structure of UniProt Q9HCS7
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 Q9UMS4
Every structure of UniProt O75934
Every structure of UniProt P09661
Every structure of UniProt P08579
Every structure of UniProt O60306
Every structure of UniProt Q9UNP9
Elsewhere: RCSB PDB 6ID0 · PDBe 6ID0 · 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 O60508 · UniProt Q2TBE0 · UniProt Q9HCS7 · UniProt P62318 · UniProt Q66K91 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt Q9UMS4 · UniProt O75934 · UniProt P09661 · UniProt P08579 · UniProt O60306 · UniProt Q9UNP9

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