SMTL ID : 9fsp.1

RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2)

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-mer

Ligands

9 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.69, C.72, C.79, H.82 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.69, A:C.72, A:C.79, A:H.82 ZN.2: 5 residues within 4Å: Chain A: C.109, C.112, C.156, H.158, C.159 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.112, A:C.156, A:H.158, A:C.159 ZN.4: 4 residues within 4Å: Chain B: C.1080, C.1083, C.1092, C.1095 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1080, B:C.1083, B:C.1092, B:C.1095 ZN.6: 4 residues within 4Å: Chain J: C.8, C.25, T.27, C.28 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.8, J:C.25, J:T.27, J:C.28 ZN.7: 6 residues within 4Å: Chain P: C.19, E.21, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.19, P:C.22, P:C.36, P:C.39 ZN.8: 4 residues within 4Å: Chain Q: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.7, Q:C.10, Q:C.44, Q:C.45 ZN.9: 4 residues within 4Å: Chain S: C.7, C.10, C.28, C.31 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.7, S:C.10, S:C.28, S:C.31 ZN.10: 5 residues within 4Å: Chain Y: C.221, S.223, H.313, C.317, H.319 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.221, Y:H.313, Y:C.317, Y:H.319 ZN.11: 5 residues within 4Å: Chain V: Q.377, L.383 Chain Y: C.380, V.382, C.383 2 PLIP interactions: 2 interactions with chain Y Metal complexes: Y:C.380, Y:C.383

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.499, D.501, D.503 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.499, A:D.499, A:D.501, A:D.501

1 x SF4: IRON/SULFUR CLUSTER(Covalent)

SF4.5: 9 residues within 4Å: Chain C: N.445 Chain F: C.287, C.290, V.292, F.293, C.296, I.302, C.307, M.310 6 PLIP interactions: 6 interactions with chain F, pi-Cation interactions: F:F.293, F:F.293 Metal complexes: F:C.287, F:C.290, F:C.296, F:C.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shah, S.Z. et al., Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters. Nat Commun (2025)

Release Date

2025-01-15

Peptides

DNA-directed RNA polymerase III subunit RPC1: A
DNA-directed RNA polymerase III subunit RPC2: B
DNA-directed RNA polymerase III subunit RPC3: C
DNA-directed RNA polymerase III subunit RPC4: D
DNA-directed RNA polymerase III subunit RPC5: E
DNA-directed RNA polymerase III subunit RPC6: F
DNA-directed RNA polymerase III subunit RPC7: G
DNA-directed RNA polymerase III subunit RPC8: H
DNA-directed RNA polymerase III subunit RPC9: I
DNA-directed RNA polymerase III subunit RPC10: J
DNA-directed RNA polymerases I and III subunit RPAC1: K
DNA-directed RNA polymerases I and III subunit RPAC2: L
DNA-directed RNA polymerases I, II, and III subunit RPABC1: M
DNA-directed RNA polymerases I, II, and III subunit RPABC2: N
DNA-directed RNA polymerases I, II, and III subunit RPABC3: O
DNA-directed RNA polymerases I, II, and III subunit RPABC4: P
DNA-directed RNA polymerases I, II, and III subunit RPABC5: Q
TATA-box-binding protein: R
Transcription factor IIIB 50 kDa subunit: S
Transcription factor TFIIIB component B'' homolog: T
snRNA-activating protein complex subunit 1: U
snRNA-activating protein complex subunit 4: V
snRNA-activating protein complex subunit 3: Y

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

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
W

Y
Z

DNA-directed RNA polymerase III subunit RPC1

DNA-directed RNA polymerase III subunit RPC2

DNA-directed RNA polymerase III subunit RPC3

DNA-directed RNA polymerase III subunit RPC4

DNA-directed RNA polymerase III subunit RPC5

DNA-directed RNA polymerase III subunit RPC6

DNA-directed RNA polymerase III subunit RPC7

DNA-directed RNA polymerase III subunit RPC8

DNA-directed RNA polymerase III subunit RPC9

DNA-directed RNA polymerase III subunit RPC10

DNA-directed RNA polymerases I and III subunit RPAC1

DNA-directed RNA polymerases I and III subunit RPAC2

DNA-directed RNA polymerases I, II, and III subunit RPABC1

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

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

DNA-directed RNA polymerases I, II, and III subunit RPABC4

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

TATA-box-binding protein

Transcription factor IIIB 50 kDa subunit

Transcription factor TFIIIB component B'' homolog

snRNA-activating protein complex subunit 1

snRNA-activating protein complex subunit 4

snRNA-activating protein complex subunit 3

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