SMTL ID : 7q4u.1

Cryo-EM structure of Mycobacterium tuberculosis RNA polymerase holoenzyme octamer comprising sigma factor SigB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-16-8-8-8-8-mer

Ligands

16 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain D: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.888, D:C.965, D:C.972, D:C.975 ZN.2: 4 residues within 4Å: Chain D: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.57, D:C.59, D:C.72, D:C.75 ZN.4: 7 residues within 4Å: Chain J: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.888, J:C.965, J:C.972, J:C.975 ZN.5: 4 residues within 4Å: Chain J: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.57, J:C.59, J:C.72, J:C.75 ZN.7: 7 residues within 4Å: Chain P: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.888, P:C.965, P:C.972, P:C.975 ZN.8: 4 residues within 4Å: Chain P: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.57, P:C.59, P:C.72, P:C.75 ZN.10: 7 residues within 4Å: Chain V: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.888, V:C.965, V:C.972, V:C.975 ZN.11: 4 residues within 4Å: Chain V: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.57, V:C.59, V:C.72, V:C.75 ZN.13: 7 residues within 4Å: Chain 1: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.888, 1:C.965, 1:C.972, 1:C.975 ZN.14: 4 residues within 4Å: Chain 1: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.57, 1:C.59, 1:C.72, 1:C.75 ZN.16: 7 residues within 4Å: Chain 7: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.888, 7:C.965, 7:C.972, 7:C.975 ZN.17: 4 residues within 4Å: Chain 7: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:C.57, 7:C.59, 7:C.72, 7:C.75 ZN.19: 7 residues within 4Å: Chain d: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.888, d:C.965, d:C.972, d:C.975 ZN.20: 4 residues within 4Å: Chain d: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:C.57, d:C.59, d:C.72, d:C.75 ZN.22: 7 residues within 4Å: Chain j: C.888, R.960, C.965, A.966, T.967, C.972, C.975 4 PLIP interactions: 4 interactions with chain j Metal complexes: j:C.888, j:C.965, j:C.972, j:C.975 ZN.23: 4 residues within 4Å: Chain j: C.57, C.59, C.72, C.75 4 PLIP interactions: 4 interactions with chain j Metal complexes: j:C.57, j:C.59, j:C.72, j:C.75

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain D: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.532, D:D.532, D:D.534, D:D.536 MG.6: 3 residues within 4Å: Chain J: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.532, J:D.532, J:D.534, J:D.536 MG.9: 3 residues within 4Å: Chain P: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:D.532, P:D.532, P:D.534, P:D.536 MG.12: 3 residues within 4Å: Chain V: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:D.532, V:D.532, V:D.534, V:D.536 MG.15: 3 residues within 4Å: Chain 1: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:D.532, 1:D.532, 1:D.534, 1:D.536 MG.18: 3 residues within 4Å: Chain 7: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain 7 Metal complexes: 7:D.532, 7:D.532, 7:D.534, 7:D.536 MG.21: 3 residues within 4Å: Chain d: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain d Metal complexes: d:D.532, d:D.532, d:D.534, d:D.536 MG.24: 3 residues within 4Å: Chain j: D.532, D.534, D.536 4 PLIP interactions: 4 interactions with chain j Metal complexes: j:D.532, j:D.532, j:D.534, j:D.536

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morichaud, Z. et al., Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Nat Commun (2023)

Release Date

2022-11-16

Peptides

DNA-directed RNA polymerase subunit alpha: ABGHMNSTYZ45abgh
DNA-directed RNA polymerase subunit beta: CIOU06ci
DNA-directed RNA polymerase subunit beta': DJPV17dj
DNA-directed RNA polymerase subunit omega: EKQW28ek
RNA polymerase sigma factor SigB: FLRX39fl

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

G
G

H
H

M
M

N
N

S
S

T
T

Y
Z

Z
AA

4
FA

5
GA

a
LA

b
MA

g
RA

h
SA

C
C

I
I

O
O

U
V

0
BA

6
HA

c
NA

i
TA

D
D

J
J

P
P

V
W

1
CA

7
IA

d
OA

j
UA

E
E

K
K

Q
Q

W
X

2
DA

8
JA

e
PA

k
VA

F
F

L
L

R
R

X
Y

3
EA

9
KA

f
QA

l
WA

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigB

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