SMTL ID : 5vi5.1

Structure of Mycobacterium smegmatis transcription initiation complex with a full transcription bubble

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

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

Ligands

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

U-C-G-A.1: 18 residues within 4Å: Chain B: T.13, C.14, G.15, A.16, G.17 Chain E: R.445, R.456, P.480, E.481, N.484, I.488, Q.605, K.875, K.883, H.1026 Chain F: R.500, D.537, D.539 Protein-ligand interaction information (PLIP) not available

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain E: R.595, R.916 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.595, E:R.916 SO4.5: 4 residues within 4Å: Chain F: R.894, G.895, K.960, R.1129 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.895 Salt bridges: F:K.960, F:R.1129 SO4.6: 3 residues within 4Å: Chain F: E.887, H.888, R.1267 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.888 Salt bridges: F:R.1267 SO4.7: 6 residues within 4Å: Chain F: D.882, V.883, T.971, G.972, R.1160, R.1164 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:G.972 Salt bridges: F:R.1160, F:R.1164 SO4.9: 3 residues within 4Å: Chain H: A.254, F.255, L.256 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F Hydrogen bonds: H:L.256, F:R.389 SO4.10: 4 residues within 4Å: Chain H: L.187, R.190, R.228, H.232 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:R.228 Salt bridges: H:R.190, H:H.232

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain F: C.890, C.967, S.969, C.974, C.977 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.890, F:C.967, F:C.974, F:C.977 ZN.4: 6 residues within 4Å: Chain F: C.60, Y.61, C.62, G.63, C.75, C.78 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.60, F:C.62, F:C.75, F:C.78

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain E: Y.1012 Chain F: V.592, A.595, S.628, R.630 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.628, F:S.628, F:R.630, E:Y.1012 EDO.11: 3 residues within 4Å: Chain H: S.406, R.408, E.409 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.406, H:S.406, H:E.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hubin, E.A. et al., Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat Commun (2017)

Release Date

2017-07-26

Peptides

DNA-directed RNA polymerase subunit alpha: CD
DNA-directed RNA polymerase subunit beta: E
DNA-directed RNA polymerase subunit beta': F
DNA-directed RNA polymerase subunit omega: G
RNA polymerase sigma factor SigA: H
RNA polymerase-binding protein RbpA: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
D

G
E

H
F

I
J

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 SigA

RNA polymerase-binding protein RbpA

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