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Cryo-EM structure of a human activated spliceosome (early bact) at 4.9 ångström.

Analyse Cryo-EM structure of a human activated spliceosome (early bact) at 4.9 ångström. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Z58
Type: protein + RNA
Length: 13,305 residues
Chains: 46
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
UniProt: Q6P2Q9, Q15029, O75643, Q96DI7, P62318, P14678, P62314, P62316, P62306, P62304, P62308, P09661, P08579, Q12874, Q15459, Q15428, O75533, Q13435, Q15393, Q15427, Q9Y3B4, Q7RTV0, Q9BWJ5, Q9BZJ0, Q99459, O15541, Q9P013, O43660, Q9HCG8, Q8TAD8, Q9Y388, Q9BRD0, Q6UX04, O60231
Ligands: IHP, GTP, MG, ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 43 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-processing-splicing factor 8	protein	2211	43% helix, 13% strand	Q6P2Q9
B	U5 snrna	rna	84	—	—
C	116 kda U5 small nuclear ribonucleoprotein component	protein	860	38% helix, 23% strand	Q15029
D	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1722	41% helix, 18% strand	O75643
E	U5 small nuclear ribonucleoprotein 40 kda protein	protein	299	0% helix, 49% strand	Q96DI7
a	Small nuclear ribonucleoprotein sm D3	protein	81	14% 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, 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
F	U6 snrna	rna	93	—	—
G	Pre-mRNA	rna	77	—	—
H	U2 snrna	rna	136	—	—
h	Small nuclear ribonucleoprotein sm D3	protein	80	14% 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
o	U2 small nuclear ribonucleoprotein a'	protein	162	27% helix, 17% strand	P09661
p	U2 small nuclear ribonucleoprotein B''	protein	165	30% helix, 25% strand	P08579
w	Splicing factor 3A subunit 3	protein	437	59% helix, 3% strand	Q12874
u	Splicing factor 3A subunit 1	protein	105	62% helix, 1% strand	Q15459
v	Splicing factor 3A subunit 2	protein	98	5% helix, 22% strand	Q15428
1	Splicing factor 3B subunit 1	protein	1038	71% helix, 0% strand	O75533
2	Splicing factor 3B subunit 2	protein	183	34% helix, 3% strand	Q13435
3	Splicing factor 3B subunit 3	protein	1177	7% helix, 45% strand	Q15393
4	Splicing factor 3B subunit 4	protein	78	26% helix, 23% strand	Q15427
5	Splicing factor 3B subunit 6	protein	108	27% helix, 22% strand	Q9Y3B4
6	Phd finger-like domain-containing protein 5A	protein	89	11% helix, 18% strand	Q7RTV0
7	Splicing factor 3B subunit 5	protein	66	59% helix, 0% strand	Q9BWJ5
J	Crooked neck-like protein 1	protein	522	73% helix, 0% strand	Q9BZJ0
L	Cell division cycle 5-like protein	protein	132	55% helix, 0% strand	Q99459
M	Ring finger protein 113A	protein	36	22% helix, 6% strand	O15541
P	Spliceosome-associated protein CWC15 homolog	protein	96	43% helix, 0% strand	Q9P013
R	Skip	protein	309	34% helix, 5% strand	—
T	Pleiotropic regulator 1	protein	313	0% helix, 48% strand	O43660
V	Pre-mRNA-splicing factor CWC22 homolog	protein	451	71% helix, 0% strand	Q9HCG8
X	Smad nuclear-interacting protein 1	protein	158	9% helix, 31% strand	Q8TAD8
Y	RNA-binding motif protein, X-linked 2	protein	104	32% helix, 25% strand	Q9Y388
Z	BUD13 homolog	protein	113	56% helix, 0% strand	Q9BRD0
z	Peptidyl-prolyl cis-trans isomerase CWC27 homolog (EC 5.2.1.8)	protein	177	12% helix, 28% strand	Q6UX04
x	Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16 (EC 3.6.4.13)	protein	583	44% helix, 20% strand	O60231

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A
GTP · Guanosine-5'-triphosphate · ligand · chains A, C
MG · Magnesium ion · metal · 6 copies · chains C, F, G, A
ZN · Zinc ion · metal · 4 copies · chains 6, G, M

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	1058	0.86	0.88	91	empty
2	930	0.85	0.87	130	empty
3	1045	0.85	0.86	97	empty
4	1025	0.85	0.86	111	empty
5	722	0.84	0.88	80	empty

Interfaces

127 interfaces between chains.

A–C · 5775 Å² buried · 75 hydrogen bonds · protein-protein
A–R · 5175 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2706 Å² buried · 41 hydrogen bonds · protein-nucleic
1–2 · 2640 Å² buried · 14 hydrogen bonds · protein-protein
3–7 · 2222 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5Z58 · Cryo-EM structure of a human activated spliceosome (early Bact) at 4.9 angstrom. · the same entry in another collection · chain f against f, 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 P09661
Every structure of UniProt P08579
Every structure of UniProt Q12874
Every structure of UniProt Q15459
Every structure of UniProt Q15428
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 Q9BZJ0
Every structure of UniProt Q99459
Every structure of UniProt O15541
Every structure of UniProt Q9P013
Every structure of UniProt O43660
Every structure of UniProt Q9HCG8
Every structure of UniProt Q8TAD8
Every structure of UniProt Q9Y388
Every structure of UniProt Q9BRD0
Every structure of UniProt Q6UX04
Every structure of UniProt O60231
Elsewhere: RCSB PDB 5Z58 · PDBe 5Z58 · UniProt Q6P2Q9 · UniProt Q15029 · UniProt O75643 · UniProt Q96DI7 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P09661 · UniProt P08579 · UniProt Q12874 · UniProt Q15459 · UniProt Q15428 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9Y3B4 · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt Q9BZJ0 · UniProt Q99459 · UniProt O15541 · UniProt Q9P013 · UniProt O43660 · UniProt Q9HCG8 · UniProt Q8TAD8 · UniProt Q9Y388 · UniProt Q9BRD0 · UniProt Q6UX04 · UniProt O60231

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