1CDW | pdb_00001cdw

HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA

• PDB DOI: https://doi.org/10.2210/pdb1CDW/pdb
• NAKB: 1CDW

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


• Deposited: 1996-04-11 Released: 1996-12-23 
• Deposition Author(s): Nikolov, D.B., Chen, H., Halay, E.D., Hoffmann, A., Roeder, R.G., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.258 (Depositor) 
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a human TATA box-binding protein/TATA element complex.

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

(1996) Proc Natl Acad Sci U S A 93: 4862-4867

• PubMed: 8643494 
• DOI: https://doi.org/10.1073/pnas.93.10.4862
• Primary Citation Related Structures: 
  1CDW


• PubMed Abstract: 
  

  The TATA box-binding protein (TBP) is required by all three eukaryotic RNA polymerases for correct initiation of transcription of ribosomal, messenger, small nuclear, and transfer RNAs. The cocrystal structure of the C-terminal/core region of human TBP complexed with the TATA element of the adenovirus major late promoter has been determined at 1.9 angstroms resolution. Structural and functional analyses of the protein-DNA complex are presented, with a detailed comparison to our 1.9-angstroms resolution structure of Arabidopsis thaliana TBP2 bound to the same TATA box.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, The Rockefeller University, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.02 kDa 
• Atom Count: 2,351 
• Modeled Residue Count: 211 
• Deposited Residue Count: 211 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TATA BINDING PROTEIN (TBP))	C [auth A]	179	Homo sapiens	Mutation(s): 0
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
DNA (5'-D(*CP*TP*GP*CP*TP*AP*TP*AP*AP*AP*AP*GP*GP*CP*TP*G)-3')	A [auth B]	16	N/A

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.258 (Depositor) 
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.8	α = 90
b = 78	β = 90
c = 97.4	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-23 
Deposition Author(s): Nikolov, D.B., Chen, H., Halay, E.D., Hoffmann, A., Roeder, R.G., Burley, S.K.

Revision History  

• Version 1.0: 1996-12-23
  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: 2024-02-07
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description