4ILU | pdb_00004ilu

Crystal structure of Mycobacterium tuberculosis CarD

• PDB DOI: https://doi.org/10.2210/pdb4ILU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-01 Released: 2013-10-30 
• Deposition Author(s): Thakur, K.G., Kaur, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.233 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture.

Kaur, G., Dutta, D., Thakur, K.G.

(2014) Proteins 82: 879-884

• PubMed: 24115125 
• DOI: https://doi.org/10.1002/prot.24419
• Primary Citation Related Structures: 
  4ILU, 4MFR


• PubMed Abstract: 
  

  Mycobacterium tuberculosis (Mtb) CarD is an essential transcriptional regulator that binds RNA polymerase and plays an important role in reprogramming transcription machinery under diverse stress conditions. Here, we report the crystal structure of CarD at 2.3 Å resolution, that represents the first structural description of CarD/CdnL-Like family of proteins. CarD adopts an overall bi-lobed structural architecture where N-terminal domain resembles 'tudor-like' domain and C-terminal domain adopts a novel five helical fold that lacks the predicted leucine zipper structural motif. The structure reveals dimeric state of CarD resulting from β-strand swapping between the N-terminal domains of each individual subunits. The structure provides crucial insights into the possible mode(s) of CarD/RNAP interactions.

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Organizational Affiliation: 
• Structural Biology Laboratory, G. N. Ramachandran Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.66 kDa 
• Atom Count: 1,408 
• Modeled Residue Count: 165 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-binding transcription factor CarD	A	170	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: carD, MT3689, Rv3583c
UniProt
Find proteins for P9WJG3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJG3  Go to UniProtKB:  P9WJG3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.233 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.5	α = 90
b = 93.5	β = 90
c = 86.51	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Thakur, K.G., Kaur, G.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2024-05-29
  Changes: Data collection