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SMTL ID : 7m8e.1

E.coli RNAP-RapA elongation complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x A- U- C- G- G- C- U- C- A: RNA (5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3')(Non-covalent)

A-U-C-G-G-C-U-C-A.1:

23 residues within 4Å:

Chain C: Q.510, R.540, Q.688, K.1065, K.1073, H.1237
Chain D: A.261, R.322, R.425, D.460, D.462, D.464
Chain H: T.13, G.14, A.15, G.16, C.17, C.18, G.19, A.20, T.21, G.22
Ligands: MG.4

Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.2:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85, D:C.88
ZN.3:	4 residues within 4Å: Chain D: C.814, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895, D:C.898

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

4 residues within 4Å:

Chain D: D.460, D.462, D.464
Ligands: A-U-C-G-G-C-U-C-A.1

4 PLIP interactions:

4 interactions with chain D

Metal complexes: D:D.460, D:D.460, D:D.462, D:D.464

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shi, W. et al., Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase. Nucleic Acids Res. (2021)

Release Date

2021-08-18

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase-associated protein RapA: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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-associated protein RapA

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