Research workbench

Cryo-EM structure of the yeast B complex at average resolution of 3.9 ångström

Analyse Cryo-EM structure of the yeast B complex at average resolution of 3.9 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZWO
Type: protein + RNA
Length: 13,774 residues
Chains: 60
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-mRNA-splicing factor 8; U4/U6 small nuclear ribonucleoprotein PRP4…
EC: 3.6.4.13
UniProt: P33334, P20053, P49704, P19735, Q03338, Q06819, P39990, P36048, P47093, P38203, P57743, Q06406, P40089, P53905, P40070, Q12420, P43321, P40018, Q02260, Q06217, Q12330, P54999, P40204, P32639, P49955, Q02554, Q04693, Q99181, Q06835, P0C074, P40565, P46947, Q07930, Q08963, P40567, P19736, P32524, Q07350, Q12368, Q00723, P38282
Ligands: GTP, MG
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 60 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-mRNA-splicing factor 8	protein	2172	44% helix, 12% strand	P33334
K	U4/U6 small nuclear ribonucleoprotein PRP4	protein	429	23% helix, 29% strand	P20053
L	Pre-mRNA-processing factor 31	protein	416	60% helix, 2% strand	P49704
N	Pre-mRNA-splicing factor 6	protein	725	68% helix, 0% strand	P19735
J	U4/U6 small nuclear ribonucleoprotein PRP3	protein	308	48% helix, 12% strand	Q03338
E	Spliceosomal protein DIB1	protein	138	36% helix, 20% strand	Q06819
M	13 kda ribonucleoprotein-associated protein	protein	126	46% helix, 14% strand	P39990
C	Pre-mRNA-splicing factor SNU114	protein	843	37% helix, 21% strand	P36048
z	U6 snrna-associated sm-like protein LSM8	protein	65	9% helix, 58% strand	P47093
q	U6 snrna-associated sm-like protein LSM2	protein	92	25% helix, 36% strand	P38203
r	U6 snrna-associated sm-like protein LSM3	protein	77	4% helix, 64% strand	P57743
x	U6 snrna-associated sm-like protein LSM6	protein	74	14% helix, 50% strand	Q06406
t	U6 snrna-associated sm-like protein LSM5	protein	77	13% helix, 49% strand	P40089
y	U6 snrna-associated sm-like protein LSM7	protein	66	6% helix, 53% strand	P53905
s	U6 snrna-associated sm-like protein LSM4	protein	77	18% helix, 49% strand	P40070
F	U6 snrna	rna	99	—	—
B	U5 snrna	rna	175	—	—
O	66 kda U4/U6.U5 small nuclear ribonucleoprotein component	protein	75	52% helix, 15% strand	Q12420
d	Small nuclear ribonucleoprotein sm D3	protein	79	19% helix, 48% strand	P43321
a	Small nuclear ribonucleoprotein-associated protein B	protein	73	7% helix, 45% strand	P40018
b	Small nuclear ribonucleoprotein sm D1	protein	77	10% helix, 44% strand	Q02260
c	Small nuclear ribonucleoprotein sm D2	protein	90	20% helix, 39% strand	Q06217
e	Small nuclear ribonucleoprotein E	protein	72	14% helix, 39% strand	Q12330
f	Small nuclear ribonucleoprotein F	protein	70	11% helix, 51% strand	P54999
g	Small nuclear ribonucleoprotein G	protein	70	4% helix, 41% strand	P40204
I	U4 snrna	rna	110	—	—
D	Pre-mRNA-splicing helicase BRR2 (EC 3.6.4.13)	protein	1699	45% helix, 17% strand	P32639
P	Small nuclear ribonucleoprotein-associated protein B	protein	70	0% helix, 57% strand	P40018
Q	Small nuclear ribonucleoprotein sm D1	protein	99	23% helix, 38% strand	Q02260
R	Small nuclear ribonucleoprotein sm D2	protein	92	22% helix, 49% strand	Q06217
S	Small nuclear ribonucleoprotein sm D3	protein	82	16% helix, 46% strand	P43321
T	Small nuclear ribonucleoprotein E	protein	77	14% helix, 48% strand	Q12330
U	Small nuclear ribonucleoprotein F	protein	73	15% helix, 58% strand	P54999
V	Small nuclear ribonucleoprotein G	protein	75	4% helix, 52% strand	P40204
G	Pre-mRNA	rna	60	—	—
1	U2 snrnp component HSH155	protein	816	75% helix, 0% strand	P49955
2	Cold sensitive U2 snrna suppressor 1	protein	211	33% helix, 5% strand	Q02554
3	Pre-mRNA-splicing factor RSE1	protein	1180	7% helix, 40% strand	Q04693
4	Protein HSH49	protein	174	29% helix, 34% strand	Q99181
5	Pre-mRNA-splicing factor RDS3	protein	103	26% helix, 15% strand	Q06835
6	RDS3 complex subunit 10	protein	84	71% helix, 0% strand	P0C074
X	U2 snrnp component IST3	protein	128	38% helix, 23% strand	P40565
Y	Pre-mRNA-splicing factor CWC26	protein	89	49% helix, 2% strand	P46947
Z	Pre-mRNA leakage protein 1	protein	22	32% helix, 0% strand	Q07930
H	U2 snrna	rna	150	—	—
h	Small nuclear ribonucleoprotein-associated protein B	protein	76	4% helix, 53% strand	P40018
i	Small nuclear ribonucleoprotein E	protein	75	19% helix, 41% strand	Q12330
j	Small nuclear ribonucleoprotein F	protein	70	14% helix, 56% strand	P54999
k	Small nuclear ribonucleoprotein G	protein	69	0% helix, 46% strand	P40204
l	Small nuclear ribonucleoprotein sm D3	protein	76	21% helix, 46% strand	P43321
m	Small nuclear ribonucleoprotein sm D1	protein	82	15% helix, 46% strand	Q02260
n	Small nuclear ribonucleoprotein sm D2	protein	65	0% helix, 55% strand	Q06217
o	U2 small nuclear ribonucleoprotein a'	protein	135	22% helix, 20% strand	Q08963
p	U2 small nuclear ribonucleoprotein B''	protein	73	32% helix, 19% strand	P40567
u	Pre-mRNA-splicing factor PRP9	protein	462	58% helix, 3% strand	P19736
w	Pre-mRNA-splicing factor PRP21	protein	127	60% helix, 1% strand	P32524
v	Pre-mRNA-splicing factor PRP11	protein	174	16% helix, 21% strand	Q07350
W	23 kda U4/U6.U5 small nuclear ribonucleoprotein component	protein	100	51% helix, 6% strand	Q12368
0	Pre-mRNA-splicing factor 38	protein	167	54% helix, 7% strand	Q00723
9	Pre-mRNA-splicing factor SPP381	protein	64	94% helix, 0% strand	P38282

Ligands and binding sites

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	1125	0.87	0.88	121	empty
2	980	0.85	0.87	174	empty
3	922	0.85	0.87	113	empty
4	1017	0.85	0.86	86	empty
5	635	0.85	0.89	138	empty

Interfaces

151 interfaces between chains.

A–C · 4754 Å² buried · 56 hydrogen bonds · protein-protein
A–N · 3790 Å² buried · 21 hydrogen bonds · protein-protein
A–L · 3698 Å² buried · 21 hydrogen bonds · protein-protein
K–J · 3125 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2964 Å² buried · 43 hydrogen bonds · protein-nucleic

Compared structures

5ZWO · Cryo-EM structure of the yeast B complex at average resolution of 3.9 angstrom · the same entry in another collection · chain r against r, 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 P33334
Every structure of UniProt P20053
Every structure of UniProt P49704
Every structure of UniProt P19735
Every structure of UniProt Q03338
Every structure of UniProt Q06819
Every structure of UniProt P39990
Every structure of UniProt P36048
Every structure of UniProt P47093
Every structure of UniProt P38203
Every structure of UniProt P57743
Every structure of UniProt Q06406
Every structure of UniProt P40089
Every structure of UniProt P53905
Every structure of UniProt P40070
Every structure of UniProt Q12420
Every structure of UniProt P43321
Every structure of UniProt P40018
Every structure of UniProt Q02260
Every structure of UniProt Q06217
Every structure of UniProt Q12330
Every structure of UniProt P54999
Every structure of UniProt P40204
Every structure of UniProt P32639
Every structure of UniProt P49955
Every structure of UniProt Q02554
Every structure of UniProt Q04693
Every structure of UniProt Q99181
Every structure of UniProt Q06835
Every structure of UniProt P0C074
Every structure of UniProt P40565
Every structure of UniProt P46947
Every structure of UniProt Q07930
Every structure of UniProt Q08963
Every structure of UniProt P40567
Every structure of UniProt P19736
Every structure of UniProt P32524
Every structure of UniProt Q07350
Every structure of UniProt Q12368
Every structure of UniProt Q00723
Every structure of UniProt P38282
Elsewhere: RCSB PDB 5ZWO · PDBe 5ZWO · UniProt P33334 · UniProt P20053 · UniProt P49704 · UniProt P19735 · UniProt Q03338 · UniProt Q06819 · UniProt P39990 · UniProt P36048 · UniProt P47093 · UniProt P38203 · UniProt P57743 · UniProt Q06406 · UniProt P40089 · UniProt P53905 · UniProt P40070 · UniProt Q12420 · UniProt P43321 · UniProt P40018 · UniProt Q02260 · UniProt Q06217 · UniProt Q12330 · UniProt P54999 · UniProt P40204 · UniProt P32639 · UniProt P49955 · UniProt Q02554 · UniProt Q04693 · UniProt Q99181 · UniProt Q06835 · UniProt P0C074 · UniProt P40565 · UniProt P46947 · UniProt Q07930 · UniProt Q08963 · UniProt P40567 · UniProt P19736 · UniProt P32524 · UniProt Q07350 · UniProt Q12368 · UniProt Q00723 · UniProt P38282

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.