5TW1

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with RbpA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA.

Hubin, E.A., Fay, A., Xu, C., Bean, J.M., Saecker, R.M., Glickman, M.S., Darst, S.A., Campbell, E.A.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.22520
  • Primary Citation of Related Structures:  
    5TW1

  • PubMed Abstract: 

    • RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters ...

    RbpA and CarD are essential transcription regulators in mycobacteria. Mechanistic analyses of promoter open complex (RPo) formation establish that RbpA and CarD cooperatively stimulate formation of an intermediate (RP2) leading to RPo; formation of RP2 is likely a bottleneck step at the majority of mycobacterial promoters. Once RPo forms, CarD also disfavors its isomerization back to RP2. We determined a 2.76 Å-resolution crystal structure of a mycobacterial transcription initiation complex (TIC) with RbpA as well as a CarD/RbpA/TIC model. Both CarD and RbpA bind near the upstream edge of the -10 element where they likely facilitate DNA bending and impede transcription bubble collapse. In vivo studies demonstrate the essential role of RbpA, show the effects of RbpA truncations on transcription and cell physiology, and indicate additional functions for RbpA not evident in vitro. This work provides a framework to understand the control of mycobacterial transcription by RbpA and CarD.

    Organizational Affiliation: 

    The Rockefeller University, New York, United States.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAA [auth J]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpA, MSMEG_3858, MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QZ11
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaB [auth A],
C [auth B],
J [auth T]		350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoA, MSMEG_1524, MSMEI_1488
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth C]1,169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoB, MSMEG_1367, MSMEI_1328
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupP60281
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth D]1,317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoC, MSMEG_1368, MSMEI_1329
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth E]107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZ, MSMEG_3053, MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QWT1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAG [auth F]466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoD, sigA, MSMEG_2758, MSMEI_2690
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideK [auth G]17Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (31-MER)H [auth O]31Aquifex aeolicus
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (26-MER)I [auth P]26Aquifex aeolicus
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
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AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
AA [auth F],
BA [auth F],
CA [auth F],
DA [auth F],
EA [auth F],
L [auth C],
M [auth C],
N [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
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Q [auth D],
R [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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FA [auth F],
O [auth C],
P [auth C],
X [auth D],
Y [auth D],
FA [auth F],
O [auth C],
P [auth C],
X [auth D],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
S [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.012α = 90
b = 161.633β = 107.72
c = 139.211γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHASERphasing
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM114450

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence