SMTL ID : 6zym.1

Human C Complex Spliceosome - High-resolution CORE

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

5 x MG: MAGNESIUM ION(Non-functional Binders)

MG.1: 3 residues within 4Å: Chain C: G.72, U.74 Chain S: G.59 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain C: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain C: G.71, U.74, G.75 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain C: G.75 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: G.46, A.47 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 12 residues within 4Å: Chain E: R.163, K.442, H.584, K.609, H.610, Y.613, Y.614, K.623, G.624 Chain Z: A.253, R.255, K.258 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain Z Hydrogen bonds: E:Y.613, E:Y.613, E:Y.614, E:G.624, E:N.1546 Salt bridges: E:R.163, E:K.442, E:K.442, E:K.442, E:H.584, E:H.584, E:K.609, E:K.609, E:K.609, E:H.610, E:K.623, E:K.623, Z:R.255, Z:K.258, Z:K.258

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Covalent)

GTP.7: 19 residues within 4Å: Chain E: P.335 Chain F: H.137, L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, C.166, D.169, G.180, P.206, G.207, H.208, K.259, D.261, Q.313 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:H.139, F:H.140, F:G.141, F:K.142, F:T.143, F:T.143, F:T.143, F:D.164, F:G.180, F:G.207, F:H.208, F:D.261, F:D.261, F:Q.313, F:Q.313 Salt bridges: F:D.169, F:K.259, F:K.259, F:K.259 pi-Stacking: F:H.139

7 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain M: C.165, C.173, C.179, H.183 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.165, M:C.173, M:C.179, M:H.183 ZN.9: 4 residues within 4Å: Chain M: C.24, C.27, C.81, C.84 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.24, M:C.27, M:C.81, M:C.84 ZN.10: 4 residues within 4Å: Chain M: C.45, C.48, C.71, C.74 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.45, M:C.48, M:C.71, M:C.74 ZN.11: 5 residues within 4Å: Chain N: C.101, C.102, C.105, C.137 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.101, N:C.102, N:C.105, N:C.137 ZN.12: 6 residues within 4Å: Chain N: C.101, C.119, C.139, C.142 Ligands: ZN.11, ZN.13 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.101, N:C.119, N:C.139, N:C.142 ZN.13: 5 residues within 4Å: Chain N: C.105, C.117, C.119, C.134 Ligands: ZN.12 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.105, N:C.117, N:C.119, N:C.134 ZN.14: 4 residues within 4Å: Chain Y: C.43, C.46, C.80, C.83 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.43, Y:C.46, Y:C.80, Y:C.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertram, K. et al., Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Mol.Cell (2020)

Release Date

2020-10-14

Peptides

Corepressor interacting with RBPJ 1: D
Pre-mRNA-processing-splicing factor 8: E
116 kDa U5 small nuclear ribonucleoprotein component: F
SNW domain-containing protein 1: G
Pleiotropic regulator 1: H
Pre-mRNA-processing factor 17: I
U5 small nuclear ribonucleoprotein 40 kDa protein: J
Cell division cycle 5-like protein: K
Crooked neck-like protein 1: L
Pre-mRNA-splicing factor RBM22: M
Protein BUD31 homolog: N
Spliceosome-associated protein CWC15 homolog: O
Serine/arginine repetitive matrix protein 2: P
Pre-mRNA-splicing factor CWC22 homolog: Q
Peptidyl-prolyl cis-trans isomerase-like 1: R
WD repeat-containing protein 70: U
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16: V
Pre-mRNA-splicing factor ISY1 homolog: W
Pre-mRNA-splicing factor CWC25 homolog: X
Splicing factor YJU2: Y
Protein FRG1: Z

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
9

E
A

F
B

G
C

H
D

I
E

J
F

K
L

L
O

M
P

N
Q

O
R

P
S

Q
T

R
V

U
p

V
r

W
s

X
t

Y
u

Z
x

Corepressor interacting with RBPJ 1

Pre-mRNA-processing-splicing factor 8

116 kDa U5 small nuclear ribonucleoprotein component

SNW domain-containing protein 1

Pleiotropic regulator 1

Pre-mRNA-processing factor 17

U5 small nuclear ribonucleoprotein 40 kDa protein

Cell division cycle 5-like protein

Crooked neck-like protein 1

Pre-mRNA-splicing factor RBM22

Protein BUD31 homolog

Spliceosome-associated protein CWC15 homolog

Serine/arginine repetitive matrix protein 2

Pre-mRNA-splicing factor CWC22 homolog

Peptidyl-prolyl cis-trans isomerase-like 1

WD repeat-containing protein 70

Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16

Pre-mRNA-splicing factor ISY1 homolog

Pre-mRNA-splicing factor CWC25 homolog

Splicing factor YJU2

Protein FRG1

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