SMTL ID : 9qeq.1

Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex

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

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.71, C.74, C.81, P.82, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.2: 4 residues within 4Å: Chain A: C.111, C.114, C.154, C.184 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:C.184 ZN.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.5: 6 residues within 4Å: Chain C: C.88, C.90, F.93, C.94, C.97 Chain R: K.718 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.88, C:C.90, C:C.94, C:C.97 ZN.6: 5 residues within 4Å: Chain I: C.17, C.20, C.39, N.41, C.42 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.17, I:C.20, I:C.39, I:C.42 ZN.7: 5 residues within 4Å: Chain I: C.86, C.89, H.91, C.114, C.119 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.86, I:C.89, I:C.114, I:C.119 ZN.8: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.44, J:C.45 ZN.9: 4 residues within 4Å: Chain L: C.19, C.22, C.36, C.39 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.19, L:C.22, L:C.36, L:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain O: U.68 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.497, A:D.499, A:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Structure of a transcribing Pol II-DSIF-SPT6-U1 snRNP complex. Nat Commun (2025)

Release Date

2025-07-09

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
RNA polymerase II subunit D: D
DNA-directed RNA polymerase II subunit E: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase subunit: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11-a: K
RNA polymerase II, I and III subunit K: L
Transcription elongation factor SPT6: M
Transcription elongation factor SPT4: Q
Transcription elongation factor SPT5: R
U1 small nuclear ribonucleoprotein 70 kDa: T
U1 small nuclear ribonucleoprotein A: U
Small nuclear ribonucleoprotein Sm D2: V
Small nuclear ribonucleoprotein F: W
Small nuclear ribonucleoprotein E: X
Small nuclear ribonucleoprotein G: Y
Small nuclear ribonucleoprotein Sm D3: Z
Small nuclear ribonucleoprotein-associated protein: 0
Small nuclear ribonucleoprotein Sm D1: 1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

Q
Y

R
Z

T
b

U
c

V
e

W
f

X
g

Y
h

Z
i

0
j

1
k

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

RNA polymerase II subunit D

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

RNA polymerase II, I and III subunit K

Transcription elongation factor SPT6

Transcription elongation factor SPT4

Transcription elongation factor SPT5

U1 small nuclear ribonucleoprotein 70 kDa

U1 small nuclear ribonucleoprotein A

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 protein

Small nuclear ribonucleoprotein Sm D1

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