SMTL ID : 6ff4.1

human Bact spliceosome core structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

MG.1: 3 residues within 4Å: Chain E: A.53, G.54, U.74 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain E: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Covalent)

IHP.5: 10 residues within 4Å: Chain H: R.163, K.442, H.584, K.606, K.609, H.610, Y.613, Y.614, K.623 Chain W: R.179 15 PLIP interactions: 14 interactions with chain H, 1 interactions with chain W Hydrogen bonds: H:Y.613, H:Y.614 Salt bridges: H:R.163, H:K.442, H:K.442, H:K.442, H:H.584, H:H.584, H:K.609, H:K.609, H:K.609, H:H.610, H:K.623, H:K.623, W:R.179

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.6: 21 residues within 4Å: Chain H: P.335 Chain I: L.138, H.139, H.140, G.141, K.142, T.143, C.144, D.164, C.166, D.169, G.178, V.179, G.207, N.258, K.259, D.261, R.262, S.311, S.312, Q.313 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:L.138, I:H.140, I:G.141, I:K.142, I:T.143, I:C.144, I:D.164, I:V.179, I:G.207, I:K.259, I:S.312, I:Q.313, I:Q.313 Salt bridges: I:K.142, I:D.261 pi-Cation interactions: I:K.259

10 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain O: C.24, C.27, C.81, C.84 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.24, O:C.27, O:C.81, O:C.84 ZN.8: 5 residues within 4Å: Chain O: C.165, W.168, C.173, C.179, R.182 3 PLIP interactions: 3 interactions with chain O Metal complexes: O:C.165, O:C.173, O:C.179 ZN.9: 5 residues within 4Å: Chain O: C.45, C.48, C.71, C.74, Q.119 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.45, O:C.48, O:C.71, O:C.74 ZN.10: 3 residues within 4Å: Chain P: C.101, C.102, C.137 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.101, P:C.102, P:C.137 ZN.11: 4 residues within 4Å: Chain P: L.100, C.101, C.119, R.140 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:C.101, P:C.119 ZN.12: 4 residues within 4Å: Chain P: C.105, C.117, C.119, C.134 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:C.105, P:C.117, P:C.134 ZN.13: 4 residues within 4Å: Chain W: C.202, C.211, C.217, H.221 3 PLIP interactions: 3 interactions with chain W Metal complexes: W:C.202, W:C.211, W:C.217 ZN.14: 5 residues within 4Å: Chain 0: C.11, K.13, C.46, C.49, C.85 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.11, 0:C.46, 0:C.49, 0:C.85 ZN.15: 5 residues within 4Å: Chain 0: C.23, C.26, C.58, I.60, C.61 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.23, 0:C.26, 0:C.58, 0:C.61 ZN.16: 5 residues within 4Å: Chain 0: C.30, C.33, D.34, C.72, C.75 3 PLIP interactions: 3 interactions with chain 0 Metal complexes: 0:C.30, 0:C.72, 0:C.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haselbach, D. et al., Structure and Conformational Dynamics of the Human Spliceosomal BactComplex. Cell (2018)

Release Date

2018-08-29

Peptides

RNA-binding motif protein, X-linked 2: A
BUD13 homolog: C
Splicing factor 3A subunit 2: F
Splicing factor 3B subunit 2: G
Pre-mRNA-processing-splicing factor 8: H
116 kDa U5 small nuclear ribonucleoprotein component: I
SNW domain-containing protein 1: J
Pleiotropic regulator 1: K
Pre-mRNA-processing factor 17: L
Cell division cycle 5-like protein: M
Crooked neck-like protein 1: N
Pre-mRNA-splicing factor RBM22: O
Protein BUD31 homolog: P
Spliceosome-associated protein CWC15 homolog: Q
Serine/arginine repetitive matrix protein 2: R
Peptidyl-prolyl cis-trans isomerase-like 1: S
Serine/arginine repetitive matrix protein 1: T
Peptidyl-prolyl cis-trans isomerase CWC27 homolog: V
RING finger protein 113A: W
Splicing factor 3B subunit 1: X
Splicing factor 3B subunit 3: Y
Splicing factor 3B subunit 5: Z
PHD finger-like domain-containing protein 5A: 0
Splicing factor 3B subunit 6: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

C
3

F
7

G
8

H
A

I
B

J
C

K
D

L
E

M
L

N
O

O
P

P
Q

Q
R

R
S

S
V

T
Y

V
s

W
t

X
u

Y
v

Z
x

0
y

1
z

RNA-binding motif protein, X-linked 2

BUD13 homolog

Splicing factor 3A subunit 2

Splicing factor 3B subunit 2

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

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

Peptidyl-prolyl cis-trans isomerase-like 1

Serine/arginine repetitive matrix protein 1

Peptidyl-prolyl cis-trans isomerase CWC27 homolog

RING finger protein 113A

Splicing factor 3B subunit 1

Splicing factor 3B subunit 3

Splicing factor 3B subunit 5

PHD finger-like domain-containing protein 5A

Splicing factor 3B subunit 6

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