3VW3

Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct

• PDB DOI: https://doi.org/10.2210/pdb3VW3/pdb
• NAKB: 3VW3

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


• Deposited: 2012-07-30 Released: 2013-03-27 
• Deposition Author(s): Yokoyama, H., Mizutani, R., Satow, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Literature

Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab

Yokoyama, H., Mizutani, R., Satow, Y.

(2013) Acta Crystallogr D Biol Crystallogr 69: 504-512

• PubMed: 23519658 
• DOI: https://doi.org/10.1107/S0907444912050007
• Primary Citation of Related Structures:  
  3VW3


• PubMed Abstract: 
  

  DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation have been implicated in mutagenesis and cancer. The crystal structure of double-stranded DNA containing the (6-4) photoproduct in complex with the anti-(6-4)-photoproduct antibody 64M-5 Fab was determined at 2.5 Å resolution. The T(6-4)T segment and the 5'-side adjacent adenosine are flipped out of the duplex and are accommodated in the concave antigen-binding pocket composed of six complementarity-determining regions (CDRs). A loop comprised of CDR L1 residues is inserted between the flipped-out T(6-4)T segment and the complementary DNA. The separation of strands by the insertion of the loop facilitates extensive and specific recognition of the photoproduct. The DNA helices flanking the T(6-4)T segment are kinked by 87°. The 64M-5 Fab recognizes the T(6-4)T segment dissociated from the complementary strand, indicating that the (6-4) photoproduct can be detected in double-stranded DNA as well as in single-stranded DNA using the 64M-5 antibody. The structure and recognition mode of the 64M-5 antibody were compared with those of the DNA (6-4) photolyase and nucleotide-excision repair protein DDB1-DDB2. These proteins have distinctive binding-site structures that are appropriate for their functions, and the flipping out of the photolesion and the kinking of the DNA are common to mutagenic (6-4) photoproducts recognized by proteins.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 58.9 kDa 
• Atom Count: 4,190 
• Modelled Residue Count: 467 
• Deposited Residue Count: 473 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)	A [auth L]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)	B [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*AP*GP*TP*GP*AP*(64T)P*(5PY)P*AP*TP*GP*GP*AP*CP*GP*G)-3')	C [auth A]	18	N/A

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*GP*TP*CP*CP*AP*TP*AP*AP*TP*CP*AP*CP*TP*CP*G)-3')	D [auth B]	18	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	E [auth H]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.290 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.43	α = 90
b = 68.43	β = 90
c = 243.658	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Yokoyama, H., Mizutani, R., Satow, Y.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2014-04-30
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description