4M61 | pdb_00004m61

Crystal structure of unliganded anti-DNA Fab A52

• PDB DOI: https://doi.org/10.2210/pdb4M61/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2013-08-08 Released: 2013-08-28 
• Deposition Author(s): Stanfield, R.L., Eilat, D., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure determination of anti-DNA Fab A52.

Stanfield, R.L., Eilat, D.

(2014) Proteins 82: 1674-1678

• PubMed: 24449198 
• DOI: https://doi.org/10.1002/prot.24514
• Primary Citation Related Structures: 
  4M61


• PubMed Abstract: 
  

  A52 is a murine monoclonal antibody isolated from autoimmune New Zealand Black/New Zealand White F1 mice that recognizes single and double stranded DNA. This mouse strain spontaneously develops systemic lupus erythematosus-like symptoms and has served as a model for that disease for many years. The 1.62 Å crystal structure of the A52 Fab fragment reveals an H3 complementarity determining region with four closely spaced arginine residues, creating a positively charged surface to accommodate bound DNA.

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Organizational Affiliation: 
• The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, 92037.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.15 kDa 
• Atom Count: 7,686 
• Modeled Residue Count: 878 
• Deposited Residue Count: 878 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab A52 light chain	A, C	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab A52 heavy chain	B, D	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth D], U [auth D], V [auth D], W [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.784	α = 90
b = 61.38	β = 96.51
c = 121.223	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Stanfield, R.L., Eilat, D., Wilson, I.A.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references
• Version 1.2: 2014-08-06
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary