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: 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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-binding protein RbpAA [auth J]114Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rbpAMSMEG_3858MSMEI_3768
UniProt
Find proteins for A0QZ11 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QZ11 
Go to UniProtKB:  A0QZ11
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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: rpoAMSMEG_1524MSMEI_1488
EC: 2.7.7.6
UniProt
Find proteins for A0QSL8 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QSL8 
Go to UniProtKB:  A0QSL8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD [auth C]1169Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoBMSMEG_1367MSMEI_1328
EC: 2.7.7.6
UniProt
Find proteins for P60281 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore P60281 
Go to UniProtKB:  P60281
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'E [auth D]1317Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoCMSMEG_1368MSMEI_1329
EC: 2.7.7.6
UniProt
Find proteins for A0QS66 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QS66 
Go to UniProtKB:  A0QS66
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaF [auth E]107Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoZMSMEG_3053MSMEI_2977
EC: 2.7.7.6
UniProt
Find proteins for A0QWT1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QWT1 
Go to UniProtKB:  A0QWT1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAG [auth F]466Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: rpoDsigAMSMEG_2758MSMEI_2690
UniProt
Find proteins for A0QW02 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QW02 
Go to UniProtKB:  A0QW02
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown peptideK [auth G]17Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (31-MER)H [auth O]31Aquifex aeolicus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (26-MER)I [auth P]26Aquifex aeolicus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth F] , BA [auth F] , CA [auth F] , DA [auth F] , EA [auth F] , L [auth C] , M [auth C] , N [auth C] , 
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

Download Ideal Coordinates CCD File 
Q [auth D], R [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
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

View Full Validation Report




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