1VOL | pdb_00001vol

TFIIB (HUMAN CORE DOMAIN)/TBP (A.THALIANA)/TATA ELEMENT TERNARY COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1VOL/pdb
• NAKB: 1VOL

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-04-29 Released: 1996-11-08 
• Deposition Author(s): Nikolov, D.B., Chen, H., Halay, E.D., Usheva, A.U., Hisatake, K., Lee, D.K., Roeder, R.G., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.318 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Crystal structure of a TFIIB-TBP-TATA-element ternary complex.

Nikolov, D.B., Chen, H., Halay, E.D., Usheva, A.A., Hisatake, K., Lee, D.K., Roeder, R.G., Burley, S.K.

(1995) Nature 377: 119-128

• PubMed: 7675079 
• DOI: https://doi.org/10.1038/377119a0
• Primary Citation Related Structures: 
  1VOL


• PubMed Abstract: 
  

  The crystal structure of the transcription factor IIB (TFIIB)/TATA box-binding protein (TBP)/TATA-element ternary complex is described at 2.7 A resolution. Core TFIIB resembles cyclin A, and recognizes the preformed TBP-DNA complex through protein-protein and protein-DNA interactions. The amino-terminal domain of core TFIIB forms the downstream surface of the ternary complex, where it could fix the transcription start site. The remaining surfaces of TBP and the TFIIB can interact with TBP-associated factors, other class II initiation factors, and transcriptional activators and coactivators.

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Organizational Affiliation: 
• Laboratories of Molecular Biophysics, Rockefeller University, New York, New York 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.96 kDa 
• Atom Count: 3,715 
• Modeled Residue Count: 423 
• Deposited Residue Count: 436 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TRANSCRIPTION FACTOR IIB (TFIIB))	C [auth A]	204	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q00403 (Homo sapiens) Explore Q00403  Go to UniProtKB:  Q00403
PHAROS:  Q00403 GTEx:  ENSG00000137947

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TATA BINDING PROTEIN (TBP))	D [auth B]	200	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P28147 (Arabidopsis thaliana) Explore P28147  Go to UniProtKB:  P28147

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*GP*CP*TP*G)-3')	A [auth C]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*GP*CP*CP*CP*TP*TP*TP*TP*AP*TP*AP*GP*CP*C)-3')	B [auth D]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.318 (Depositor) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.9	α = 90
b = 78	β = 90
c = 134.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Nikolov, D.B., Chen, H., Halay, E.D., Usheva, A.U., Hisatake, K., Lee, D.K., Roeder, R.G., Burley, S.K.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-05-22
  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: 2024-02-14
  Changes: Data collection, Database references