1BC7

SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BC7/pdb
• NAKB: 1BC7

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


• Deposited: 1998-05-05 Released: 1999-01-21 
• Deposition Author(s): Mo, Y., Vaessen, B., Johnston, K., Marmorstein, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.286 
• R-Value Work: 0.222 

Starting Model: experimental

Literature

Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins.

Mo, Y., Vaessen, B., Johnston, K., Marmorstein, R.

(1998) Mol Cell 2: 201-212

• PubMed: 9734357 
• DOI: https://doi.org/10.1016/s1097-2765(00)80130-6
• Primary Citation of Related Structures:  
  1BC7, 1BC8


• PubMed Abstract: 
  

  SAP-1 is a member of the Ets transcription factors and cooperates with SRF protein to activate transcription of the c-fos protooncogene. The crystal structures of the conserved ETS domain of SAP-1 bound to DNA sequences from the E74 and c-fos promoters reveal that a set of conserved residues contact a GGA core DNA sequence. Discrimination for sequences outside this core is mediated by DNA contacts from conserved and nonconserved protein residues and sequence-dependent DNA structural properties characteristic of A-form DNA structure. Comparison with the related PU.1/DNA and GABPalpha/beta/DNA complexes provides general insights into DNA discrimination between Ets proteins. Modeling studies of a SAP-1/SRF/DNA complex suggest that SRF may modulate SAP-1 binding to DNA by interacting with its ETS domain.

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Organizational Affiliation: 

The Wistar Institute, Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.93 kDa 
• Atom Count: 1,372 
• Modelled Residue Count: 115 
• Deposited Residue Count: 115 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ETS-DOMAIN PROTEIN)	C	93	Homo sapiens	Mutation(s): 0  Gene Names: SAP-1 RESIDUES 1-93
UniProt & NIH Common Fund Data Resources
Find proteins for P28324 (Homo sapiens) Explore P28324  Go to UniProtKB:  P28324
PHAROS:  P28324 GTEx:  ENSG00000158711

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*AP*GP*GP*AP*TP*GP*TP*G)-3')	A	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*TP*GP*TP*C)-3')	B	11	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.286 
• R-Value Work: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.503	α = 90
b = 62.306	β = 107.17
c = 38.865	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-21 
Deposition Author(s): Mo, Y., Vaessen, B., Johnston, K., Marmorstein, R.

Revision History  

• Version 1.0: 1999-01-21
  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: 2024-02-07
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description