SMTL ID : 6ff7.1

human Bact spliceosome core structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-4-1-1-1-1-1-1-2-2-2-2-2-2-2-1-1-1-1-1-mer

Ligands

11 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain 3: C.408, C.411 Chain B: C.61, U.62 No protein-ligand interaction detected (PLIP) ZN.8: 4 residues within 4Å: Chain O: C.27, C.81, T.83, C.84 No protein-ligand interaction detected (PLIP) ZN.9: 2 residues within 4Å: Chain O: C.173, C.179 No protein-ligand interaction detected (PLIP) ZN.10: 3 residues within 4Å: Chain O: C.45, C.71, C.74 No protein-ligand interaction detected (PLIP) ZN.11: 3 residues within 4Å: Chain P: C.101, C.102, C.137 No protein-ligand interaction detected (PLIP) ZN.12: 2 residues within 4Å: Chain P: L.100, C.101 No protein-ligand interaction detected (PLIP) ZN.13: 3 residues within 4Å: Chain P: C.117, C.119, C.134 No protein-ligand interaction detected (PLIP) ZN.14: 4 residues within 4Å: Chain U: G.243 Chain W: C.202, C.211, C.217 No protein-ligand interaction detected (PLIP) ZN.15: 5 residues within 4Å: Chain 0: C.11, C.46, C.49, C.85, K.87 No protein-ligand interaction detected (PLIP) ZN.16: 3 residues within 4Å: Chain 0: C.26, C.58, C.61 No protein-ligand interaction detected (PLIP) ZN.17: 4 residues within 4Å: Chain 0: C.30, C.33, C.72, C.75 No protein-ligand interaction detected (PLIP)

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

MG.2: 4 residues within 4Å: Chain E: A.53, G.54, U.74 Chain U: G.243 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain E: G.75 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain E: G.54, C.55, G.71 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: ADP.19 No protein-ligand interaction detected (PLIP)

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.6: 1 residues within 4Å: Chain H: K.623 No protein-ligand interaction detected (PLIP)

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

GTP.7: 13 residues within 4Å: Chain I: L.138, H.139, H.140, G.141, K.142, T.143, C.144, G.178, V.179, R.262, S.311, S.312, Q.313 10 PLIP interactions: 10 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:V.179, I:V.179, I:S.312, I:Q.313

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.18: 7 residues within 4Å: Chain w: T.480, N.482, G.506, A.507, G.508, K.509, T.510 6 PLIP interactions: 6 interactions with chain w Hydrogen bonds: w:T.480, w:N.482, w:G.506, w:G.508, w:K.509, w:T.510 ADP.19: 11 residues within 4Å: Ligands: MG.20 Chain w: F.1325, F.1327, F.1328, T.1352, G.1353, S.1354, G.1355, K.1356, T.1357, P.1694 7 PLIP interactions: 7 interactions with chain w Hydrogen bonds: w:F.1327, w:N.1329, w:G.1353, w:S.1354, w:G.1355, w:K.1356, w:T.1357

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

2019-03-13

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: 1y
Smad nuclear-interacting protein 1: 2
Splicing factor 3A subunit 3: 3
U5 small nuclear ribonucleoprotein 40 kDa protein: 4
Pre-mRNA-processing factor 19: 5678
Pre-mRNA-splicing factor SPF27: 9
Pre-mRNA-splicing factor SYF1: a
Pre-mRNA-splicing factor CWC22 homolog: b
Intron-binding protein aquarius: c
U2 small nuclear ribonucleoprotein A': d
U2 small nuclear ribonucleoprotein B'': e
Small nuclear ribonucleoprotein Sm D2: fm
Small nuclear ribonucleoprotein F: gn
Small nuclear ribonucleoprotein E: ho
Small nuclear ribonucleoprotein G: ip
Small nuclear ribonucleoprotein Sm D3: jq
Small nuclear ribonucleoprotein-associated proteins B and B': kr
Small nuclear ribonucleoprotein Sm D1: ls
Peptidyl-prolyl cis-trans isomerase E: t
Splicing factor 3A subunit 1: u
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16: v
U5 small nuclear ribonucleoprotein 200 kDa helicase: w
Pre-mRNA-splicing factor ISY1 homolog: x

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

y
N

2
0

3
9

4
F

5
G

6
H

7
I

8
J

9
K

a
M

b
T

c
U

d
W

e
X

f
a

m
h

g
b

n
i

h
c

o
j

i
d

p
k

j
e

q
l

k
f

r
m

l
g

s
n

t
o

u
p

v
q

w
r

x
w

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

Smad nuclear-interacting protein 1

Splicing factor 3A subunit 3

U5 small nuclear ribonucleoprotein 40 kDa protein

Pre-mRNA-processing factor 19

Pre-mRNA-splicing factor SPF27

Pre-mRNA-splicing factor SYF1

Pre-mRNA-splicing factor CWC22 homolog

Intron-binding protein aquarius

U2 small nuclear ribonucleoprotein A'

U2 small nuclear ribonucleoprotein B''

Small nuclear ribonucleoprotein Sm D2

Small nuclear ribonucleoprotein F

Small nuclear ribonucleoprotein E

Small nuclear ribonucleoprotein G

Small nuclear ribonucleoprotein Sm D3

Small nuclear ribonucleoprotein-associated proteins B and B'

Small nuclear ribonucleoprotein Sm D1

Peptidyl-prolyl cis-trans isomerase E

Splicing factor 3A subunit 1

Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX16

U5 small nuclear ribonucleoprotein 200 kDa helicase

Pre-mRNA-splicing factor ISY1 homolog

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