1BC8

STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

• PDB DOI: https://doi.org/10.2210/pdb1BC8/pdb
• NAKB: 1BC8

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


• Deposited: 1998-05-05 Released: 1998-12-01 
• Deposition Author(s): Mo, Y., Vaessen, B., Johnston, K., Marmorstein, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

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: 17.44 kDa 
• Atom Count: 1,356 
• Modelled Residue Count: 113 
• Deposited Residue Count: 113 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SAP-1 ETS DOMAIN)	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(*TP*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')	A	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')	B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B], E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.277 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.59	α = 90
b = 55.67	β = 107.16
c = 44.23	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-01 
Deposition Author(s): Mo, Y., Vaessen, B., Johnston, K., Marmorstein, R.

Revision History  

• Version 1.0: 1998-12-01
  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, Derived calculations