1JFI | pdb_00001jfi

Crystal Structure of the NC2-TBP-DNA Ternary Complex

• PDB DOI: https://doi.org/10.2210/pdb1JFI/pdb
• NAKB: 1JFI

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-06-20 Released: 2001-07-11 
• Deposition Author(s): Kamada, K., Shu, F., Chen, H., Malik, S., Stelzer, G., Roeder, R.G., Meisterernst, M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex.

Kamada, K., Shu, F., Chen, H., Malik, S., Stelzer, G., Roeder, R.G., Meisterernst, M., Burley, S.K.

(2001) Cell 106: 71-81

• PubMed: 11461703 
• DOI: https://doi.org/10.1016/s0092-8674(01)00417-2
• Primary Citation Related Structures: 
  1JFI


• PubMed Abstract: 
  

  The X-ray structure of a ternary complex of Negative Cofactor 2 (NC2), the TATA box binding protein (TBP), and DNA has been determined at 2.6 A resolution. The N termini of NC2 alpha and beta resemble histones H2A and H2B, respectively, and form a heterodimer that binds to the bent DNA double helix on the underside of the preformed TBP-DNA complex via electrostatic interactions. NC2beta contributes to inhibition of TATA-dependent transcription through interactions of its C-terminal alpha helix with a conserved hydrophobic feature on the upper surface of TBP, which in turn positions the penultimate alpha helix of NC2beta to block recognition of the TBP-DNA complex by transcription factor IIB. Further regulatory implications of the NC2 heterodimer structure are discussed.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, 1230 York Avenue, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.08 kDa 
• Atom Count: 3,743 
• Modeled Residue Count: 417 
• Deposited Residue Count: 500 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription Regulator NC2 alpha chain	C [auth A]	98	Homo sapiens	Mutation(s): 0  Gene Names: NC2 alpha (DRAP1)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14919 (Homo sapiens) Explore Q14919  Go to UniProtKB:  Q14919
PHAROS:  Q14919 GTEx:  ENSG00000175550

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription Regulator NC2 beta chain	D [auth B]	179	Homo sapiens	Mutation(s): 0  Gene Names: NC2 beta (Dr1)
UniProt & NIH Common Fund Data Resources
Find proteins for Q01658 (Homo sapiens) Explore Q01658  Go to UniProtKB:  Q01658
PHAROS:  Q01658 GTEx:  ENSG00000117505

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-BOX-BINDING PROTEIN (TBP)	E [auth C]	185	Homo sapiens	Mutation(s): 0  Gene Names: tbp
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens) Explore P20226  Go to UniProtKB:  P20226
PHAROS:  P20226 GTEx:  ENSG00000112592

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*CP*C)-3'	A [auth D]	19	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*G*GP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*CP*AP*A)-3'	B [auth E]	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.684	α = 90
b = 119.075	β = 90
c = 155.076	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-07-11 
Deposition Author(s): Kamada, K., Shu, F., Chen, H., Malik, S., Stelzer, G., Roeder, R.G., Meisterernst, M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2001-07-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description