SMTL ID : 7dco.1

Cryo-EM structure of the activated spliceosome (Bact complex) at an atomic resolution of 2.5 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 11 residues within 4Å: Chain A: R.236, K.517, Y.655, H.659, K.681, K.684, H.685, Y.688, N.692, K.697, G.698 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Y.688, A:N.692, A:G.698 Water bridges: A:K.681, A:G.698 Salt bridges: A:R.236, A:K.517, A:K.517, A:K.517, A:H.659, A:H.659, A:K.681, A:K.684, A:K.684, A:K.684, A:H.685, A:K.697

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

GTP.2: 19 residues within 4Å: Chain C: P.141, L.142, H.143, S.144, G.145, K.146, T.147, S.148, L.189, S.190, G.217, N.268, K.269, D.271, R.272, S.315, T.316, K.317 Ligands: MG.3 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:H.143, C:S.144, C:G.145, C:K.146, C:T.147, C:T.147, C:S.148, C:S.148, C:S.190, C:G.217, C:K.269, C:K.269, C:T.316, C:K.317 Water bridges: C:H.143, C:S.190, C:S.190 Salt bridges: C:H.143, C:K.146, C:K.146, C:D.271

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 3 residues within 4Å: Chain C: T.147, S.190 Ligands: GTP.2 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.147, C:S.190, H2O.28, H2O.28 MG.5: 2 residues within 4Å: Chain L: A.59, G.60 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain L: G.81 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain L: G.81 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain L: G.60, C.61, G.77 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain 2: S.1047, T.1067, P.1068, I.1071 3 PLIP interactions: 3 interactions with chain 2 Metal complexes: 2:T.1067, 2:P.1068, 2:I.1071

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain C: T.321, E.326, F.429, R.430, Q.431 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.321, C:E.326, C:Q.431

15 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain X: C.423, I.425, C.426, H.440, H.446 4 PLIP interactions: 4 interactions with chain X Metal complexes: X:C.423, X:C.426, X:H.440, X:H.446 ZN.10: 4 residues within 4Å: Chain X: C.282, C.285, H.298, H.304 5 PLIP interactions: 5 interactions with chain X Metal complexes: X:C.282, X:C.285, X:H.298, X:H.304, X:H.304 ZN.11: 4 residues within 4Å: Chain Z: C.68, C.71, H.84, H.90 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.68, Z:C.71, Z:H.84, Z:H.90 ZN.13: 4 residues within 4Å: Chain 4: C.11, C.46, C.49, C.86 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.11, 4:C.46, 4:C.49, 4:C.86 ZN.14: 4 residues within 4Å: Chain 4: C.23, C.26, C.58, C.61 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.23, 4:C.26, 4:C.58, 4:C.61 ZN.15: 4 residues within 4Å: Chain 4: C.30, C.33, C.73, C.76 4 PLIP interactions: 4 interactions with chain 4 Metal complexes: 4:C.30, 4:C.33, 4:C.73, 4:C.76 ZN.16: 6 residues within 4Å: Ligands: ZN.17, ZN.18 Chain c: C.104, C.105, C.108, C.148 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.104, c:C.105, c:C.108, c:C.148 ZN.17: 6 residues within 4Å: Ligands: ZN.16, ZN.18 Chain c: C.104, C.122, C.150, C.153 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.104, c:C.122, c:C.150, c:C.153 ZN.18: 6 residues within 4Å: Ligands: ZN.16, ZN.17 Chain c: C.108, C.120, C.122, C.145 4 PLIP interactions: 4 interactions with chain c Metal complexes: c:C.108, c:C.120, c:C.122, c:C.145 ZN.19: 4 residues within 4Å: Chain f: C.13, C.16, C.71, C.74 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.13, f:C.16, f:C.71, f:C.74 ZN.20: 4 residues within 4Å: Chain f: C.34, C.37, C.61, C.64 4 PLIP interactions: 4 interactions with chain f Metal complexes: f:C.34, f:C.37, f:C.61, f:C.64 ZN.21: 4 residues within 4Å: Chain g: C.73, C.81, C.87, H.91 4 PLIP interactions: 4 interactions with chain g Metal complexes: g:C.73, g:C.81, g:C.87, g:H.91 ZN.22: 4 residues within 4Å: Chain o: C.144, C.153, C.159, H.163 4 PLIP interactions: 4 interactions with chain o Metal complexes: o:C.144, o:C.153, o:C.159, o:H.163 ZN.23: 4 residues within 4Å: Chain o: C.199, C.202, C.219, C.222 4 PLIP interactions: 4 interactions with chain o Metal complexes: o:C.199, o:C.202, o:C.219, o:C.222 ZN.24: 4 residues within 4Å: Chain o: C.214, H.216, C.233, C.236 4 PLIP interactions: 4 interactions with chain o Metal complexes: o:C.214, o:H.216, o:C.233, o:C.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, R. et al., Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Science (2021)

Release Date

2021-03-17

Peptides

PRP8 isoform 1: A
SNU114 isoform 1: C
BRR2 isoform 1: D
Small nuclear ribonucleoprotein Sm D3: E
BJ4_G0014900.mRNA.1.CDS.1: FQ
SMD1 isoform 1: GV
BJ4_G0037700.mRNA.1.CDS.1: HW
Small nuclear ribonucleoprotein E: IR
Sm protein F: JS
Small nuclear ribonucleoprotein G: KT
HLJ1_G0053790.mRNA.1.CDS.1: O
BJ4_G0027490.mRNA.1.CDS.1: P
Small nuclear ribonucleoprotein Sm D3: U
PRP9 isoform 1: X
Pre-mRNA-splicing factor PRP21: Y
PRP11 isoform 1: Z
HSH155 isoform 1: 0
HLJ1_G0043010.mRNA.1.CDS.1: 1
RSE1 isoform 1: 2
HSH49 isoform 1: 3
BJ4_G0056610.mRNA.1.CDS.1: 4
RDS3 complex subunit 10: 5
Pre-mRNA-splicing factor CEF1: 6
Pre-mRNA-processing factor 19: 789a
SNT309 isoform 1: b
BUD31 isoform 1: c
HLJ1_G0054350.mRNA.1.CDS.1: d
Pre-mRNA-processing protein 45: e
Pre-mRNA-splicing factor SLT11: f
Pre-mRNA-splicing factor CWC2: g
Pre-mRNA-splicing factor CWC15: h
Pre-mRNA leakage protein 1: i
SX2_G0027210.mRNA.1.CDS.1: j
Pre-mRNA-splicing factor CWC26: k
CDC40 isoform 1: l
Pre-mRNA-splicing factor CWC21: m
CWC22 isoform 1: n
Pre-mRNA-splicing factor CWC24: o
CWC27 isoform 1: p
Pre-mRNA-splicing factor SPP2: q
CLF1 isoform 1: r
SYF1 isoform 1: s
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2: t

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

D
D

E
d

F
a

Q
h

G
b

V
m

H
c

W
n

I
e

R
i

J
f

S
j

K
g

T
k

O
o

P
p

U
l

X
u

Y
w

Z
v

0
1

1
2

2
3

3
4

4
5

5
6

6
L

7
s

8
t

9
q

a
r

b
K

c
N

d
T

e
P

f
Q

g
R

h
S

i
Y

j
X

k
Z

l
W

m
U

n
V

o
M

p
z

q
y

r
J

s
I

t
x

PRP8 isoform 1

SNU114 isoform 1

BRR2 isoform 1

Small nuclear ribonucleoprotein Sm D3

BJ4_G0014900.mRNA.1.CDS.1

SMD1 isoform 1

BJ4_G0037700.mRNA.1.CDS.1

Small nuclear ribonucleoprotein E

Sm protein F

Small nuclear ribonucleoprotein G

HLJ1_G0053790.mRNA.1.CDS.1

BJ4_G0027490.mRNA.1.CDS.1

Small nuclear ribonucleoprotein Sm D3

PRP9 isoform 1

Pre-mRNA-splicing factor PRP21

PRP11 isoform 1

HSH155 isoform 1

HLJ1_G0043010.mRNA.1.CDS.1

RSE1 isoform 1

HSH49 isoform 1

BJ4_G0056610.mRNA.1.CDS.1

RDS3 complex subunit 10

Pre-mRNA-splicing factor CEF1

Pre-mRNA-processing factor 19

SNT309 isoform 1

BUD31 isoform 1

HLJ1_G0054350.mRNA.1.CDS.1

Pre-mRNA-processing protein 45

Pre-mRNA-splicing factor SLT11

Pre-mRNA-splicing factor CWC2

Pre-mRNA-splicing factor CWC15

Pre-mRNA leakage protein 1

SX2_G0027210.mRNA.1.CDS.1

Pre-mRNA-splicing factor CWC26

CDC40 isoform 1

Pre-mRNA-splicing factor CWC21

CWC22 isoform 1

Pre-mRNA-splicing factor CWC24

CWC27 isoform 1

Pre-mRNA-splicing factor SPP2

CLF1 isoform 1

SYF1 isoform 1

Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2

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