SMTL ID : 6kf4.1

Cryo-EM structure of Thermococcus kodakarensis RNA polymerase

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: R.426, D.461, D.463, D.465 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.461, A:D.461, A:D.465, A:D.465

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.60, E.61, C.63, C.70, H.73 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.60, A:H.73 ZN.3: 4 residues within 4Å: Chain A: C.103, C.147, H.149, C.150 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.147, A:H.149, A:C.150 ZN.4: 4 residues within 4Å: Chain B: C.1065, C.1068, C.1083, C.1086 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1065, B:C.1068, B:C.1083, B:C.1086 ZN.5: 4 residues within 4Å: Chain J: C.7, C.10, C.44, C.45 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.10, J:C.44, J:C.44 ZN.6: 5 residues within 4Å: Chain K: C.11, G.12, E.14, C.27, C.30 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.11, K:E.14, K:C.27, K:C.30 ZN.7: 6 residues within 4Å: Chain L: C.117, G.118, T.119, H.122, C.140, K.142 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:C.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jun, S.H. et al., Direct binding of TFE alpha opens DNA binding cleft of RNA polymerase. Nat Commun (2020)

Release Date

2020-07-01

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase subunit A'': C
DNA-directed RNA polymerase subunit D: D
DNA-directed RNA polymerase, subunit E: E
DNA-directed RNA polymerase, subunit F: F
DNA-directed RNA polymerase subunit H: G
DNA-directed RNA polymerase subunit K: H
DNA-directed RNA polymerase subunit L: I
DNA-directed RNA polymerase subunit N: J
DNA-directed RNA polymerase subunit P: K
Transcription factor E: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
K

I
L

J
N

K
P

L
G

DNA-directed RNA polymerase subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit A''

DNA-directed RNA polymerase subunit D

DNA-directed RNA polymerase, subunit E

DNA-directed RNA polymerase, subunit F

DNA-directed RNA polymerase subunit H

DNA-directed RNA polymerase subunit K

DNA-directed RNA polymerase subunit L

DNA-directed RNA polymerase subunit N

DNA-directed RNA polymerase subunit P

Transcription factor E

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