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The cryo-EM structure of the precusor of human pre-catalytic spliceosome (pre-B complex)

Analyse The cryo-EM structure of the precusor of human pre-catalytic spliceosome (pre-B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AH0
Type: protein + RNA
Length: 13,870 residues
Chains: 57
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U5SNRNA; U5 small nuclear ribonucleoprotein 200 kda helicase; U5 small nuclear…
EC: 3.6.4.13
UniProt: O75643, Q96DI7, P62316, P62306, P62304, P62308, P62318, P14678, P62314, Q9Y333, P62310, Q9Y4Z0, Q9Y4Y9, P62312, Q9UK45, O95777, P09661, P08579, Q15459, Q15428, Q12874, O75533, Q13435, Q15393, Q15427, Q9Y3B4, Q7RTV0, Q9BWJ5, O43395, O43172, O94906, Q8WWY3, P55769, P83876, Q53GS9, Q9BUQ8, Q6P2Q9, Q15029
Ligands: IHP, GTP, MG
Pockets: 20 · best druggability 0.75

Structure

electron microscopy · 56 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	U5SNRNA	rna	115	—	—
D	U5 small nuclear ribonucleoprotein 200 kda helicase (EC 3.6.4.13)	protein	1874	45% helix, 16% strand	O75643
E	U5 small nuclear ribonucleoprotein 40 kda protein	protein	299	0% helix, 49% strand	Q96DI7
a	Small nuclear ribonucleoprotein sm D2	protein	78	14% helix, 47% strand	P62316
b	Small nuclear ribonucleoprotein F	protein	73	14% helix, 52% strand	P62306
c, R	Small nuclear ribonucleoprotein E	protein	78	8% helix, 44% strand	P62304
d	Small nuclear ribonucleoprotein G	protein	69	12% helix, 46% strand	P62308
e	Small nuclear ribonucleoprotein sm D3	protein	78	10% helix, 49% strand	P62318
f	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	64	0% helix, 56% strand	P14678
g	Small nuclear ribonucleoprotein sm D1	protein	93	19% helix, 40% strand	P62314
F	U6SNRNA	rna	69	—	—
q	U6 snrna-associated sm-like protein LSM2	protein	90	26% helix, 36% strand	Q9Y333
r	U6 snrna-associated sm-like protein LSM3	protein	75	8% helix, 57% strand	P62310
s	U6 snrna-associated sm-like protein LSM4	protein	74	20% helix, 49% strand	Q9Y4Z0
t	U6 snrna-associated sm-like protein LSM5	protein	75	13% helix, 48% strand	Q9Y4Y9
x	U6 snrna-associated sm-like protein LSM6	protein	70	10% helix, 50% strand	P62312
y	U6 snrna-associated sm-like protein LSM7	protein	65	5% helix, 55% strand	Q9UK45
z	U6 snrna-associated sm-like protein LSM8	protein	61	10% helix, 61% strand	O95777
G	Pre-mRNA	rna	42	—	—
H	U2SNRNA	rna	109	—	—
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
h	Small nuclear ribonucleoprotein sm D3	protein	80	14% helix, 49% strand	P62318
i	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	73	10% helix, 55% strand	P14678
j	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	74	15% helix, 57% strand	P62306
l	Small nuclear ribonucleoprotein E	protein	79	18% helix, 58% strand	P62304
n	Small nuclear ribonucleoprotein G	protein	68	9% helix, 56% strand	P62308
u	Splicing factor 3A subunit 1	protein	124	63% helix, 1% strand	Q15459
v	Splicing factor 3A subunit 2	protein	99	5% helix, 22% strand	Q15428
w	Splicing factor 3A subunit 3	protein	443	60% helix, 3% strand	Q12874
1	Splicing factor 3B subunit 1	protein	1030	71% helix, 0% strand	O75533
2	Splicing factor 3B subunit 2	protein	186	31% helix, 5% strand	Q13435
3	Splicing factor 3B subunit 3	protein	1174	7% helix, 43% strand	Q15393
4	Splicing factor 3B subunit 4	protein	78	24% helix, 38% strand	Q15427
5	Splicing factor 3B subunit 6	protein	108	26% helix, 22% strand	Q9Y3B4
6	Phd finger-like domain-containing protein 5A	protein	89	16% helix, 20% strand	Q7RTV0
7	Splicing factor 3B subunit 5	protein	66	59% helix, 0% strand	Q9BWJ5
J	U4/U6 small nuclear ribonucleoprotein PRP3	protein	167	37% helix, 20% strand	O43395
K	U4/U6 small nuclear ribonucleoprotein PRP4	protein	343	12% helix, 40% strand	O43172
N	Pre-mRNA-processing factor 6	protein	579	70% helix, 0% strand	O94906
L	U4/U6 small nuclear ribonucleoprotein PRP31	protein	226	73% helix, 0% strand	Q8WWY3
M	NHP2-like protein 1	protein	125	48% helix, 15% strand	P55769
O	Thioredoxin-like protein 4A	protein	139	30% helix, 19% strand	P83876
W	U4/U6.U5 tri-snrnp-associated protein 2	protein	463	23% helix, 20% strand	Q53GS9
I	U4SNRNA	rna	117	—	—
P	Small nuclear ribonucleoprotein sm D2	protein	74	15% helix, 46% strand	P62316
Q	Small nuclear ribonucleoprotein F	protein	71	10% helix, 51% strand	P62306
S	Small nuclear ribonucleoprotein G	protein	73	11% helix, 45% strand	P62308
T	Small nuclear ribonucleoprotein sm D3	protein	71	10% helix, 54% strand	P62318
U	Small nuclear ribonucleoprotein-associated proteins B and B'	protein	64	0% helix, 55% strand	P14678
V	Small nuclear ribonucleoprotein sm D1	protein	82	9% helix, 41% strand	P62314
X	Probable ATP-dependent RNA helicase DDX23 (EC 3.6.4.13)	protein	414	47% helix, 14% strand	Q9BUQ8
A	Pre-mRNA-processing-splicing factor 8	protein	2221	43% helix, 11% strand	Q6P2Q9
C	116 kda U5 small nuclear ribonucleoprotein component	protein	818	38% helix, 21% strand	Q15029

Ligands and binding sites

IHP · Inositol hexakisphosphate · ligand · chains A
GTP · Guanosine-5'-triphosphate · ligand · chains A, C
MG · Magnesium ion · metal · chains C

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	1154	0.75	0.79	135	empty
2	905	0.75	0.79	109	empty
3	859	0.75	0.80	98	empty
4	758	0.74	0.80	87	empty
5	913	0.73	0.78	115	empty

Interfaces

105 interfaces between chains.

F–I · 1511 Å² buried · 116 hydrogen bonds · nucleic-nucleic
A–C · 1257 Å² buried · 18 hydrogen bonds · protein-protein
B–A · 1041 Å² buried · 21 hydrogen bonds · protein-nucleic
G–H · 774 Å² buried · 73 hydrogen bonds · nucleic-nucleic
F–H · 575 Å² buried · 60 hydrogen bonds · nucleic-nucleic

Compared structures

6AH0 · The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) · the same entry in another collection · chain b against b, 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 O75643
Every structure of UniProt Q96DI7
Every structure of UniProt P62316
Every structure of UniProt P62306
Every structure of UniProt P62304
Every structure of UniProt P62308
Every structure of UniProt P62318
Every structure of UniProt P14678
Every structure of UniProt P62314
Every structure of UniProt Q9Y333
Every structure of UniProt P62310
Every structure of UniProt Q9Y4Z0
Every structure of UniProt Q9Y4Y9
Every structure of UniProt P62312
Every structure of UniProt Q9UK45
Every structure of UniProt O95777
Every structure of UniProt P09661
Every structure of UniProt P08579
Every structure of UniProt Q15459
Every structure of UniProt Q15428
Every structure of UniProt Q12874
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 O43395
Every structure of UniProt O43172
Every structure of UniProt O94906
Every structure of UniProt Q8WWY3
Every structure of UniProt P55769
Every structure of UniProt P83876
Every structure of UniProt Q53GS9
Every structure of UniProt Q9BUQ8
Every structure of UniProt Q6P2Q9
Every structure of UniProt Q15029
Elsewhere: RCSB PDB 6AH0 · PDBe 6AH0 · UniProt O75643 · UniProt Q96DI7 · UniProt P62316 · UniProt P62306 · UniProt P62304 · UniProt P62308 · UniProt P62318 · UniProt P14678 · UniProt P62314 · UniProt Q9Y333 · UniProt P62310 · UniProt Q9Y4Z0 · UniProt Q9Y4Y9 · UniProt P62312 · UniProt Q9UK45 · UniProt O95777 · UniProt P09661 · UniProt P08579 · UniProt Q15459 · UniProt Q15428 · UniProt Q12874 · UniProt O75533 · UniProt Q13435 · UniProt Q15393 · UniProt Q15427 · UniProt Q9Y3B4 · UniProt Q7RTV0 · UniProt Q9BWJ5 · UniProt O43395 · UniProt O43172 · UniProt O94906 · UniProt Q8WWY3 · UniProt P55769 · UniProt P83876 · UniProt Q53GS9 · UniProt Q9BUQ8 · UniProt Q6P2Q9 · UniProt Q15029

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