Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48690.40 
• Atom Count: 3386 
• Residue Count: 440 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

1KEG

Antibody 64M-2 Fab complexed with dTT(6-4)TT

• DOI: 10.2210/pdb1KEG/pdb
• NDB: PD0276

• Classification: IMMUNE SYSTEM/DNA


• Deposited: 2001-11-15 Released: 2002-11-15 
• Deposition Author(s): Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E., Nikaido, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 

Literature

Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides.

Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E., Nikaido, O.

(2012) Acta Crystallogr.,Sect.D 68: 232-238

• PubMed: 22349224 
• DOI: 10.1107/S0907444912000327
• Also Cited By: 3VW3


• PubMed Abstract: 
  

Pyrimidine (6-4) pyrimidone DNA photoproducts produced by ultraviolet light are highly mutagenic and carcinogenic. The crystal structure of the dTT(6-4)TT photoproduct in complex with the Fab fragment of the antibody 64M-2 that is specific for (6-4) photoproducts was determined at 2.4 Å resolution. The dT(6-4)T segment is fully accommodated in the concave binding pocket of the Fab, as observed in the complex of dT(6-4)T with the Fab. The pyrimidine and pyrimidone bases of the dT(6-4)T segment are positioned nearly perpendicularly to each other. The thymidine segments flanking both ends extend away from the dT(6-4)T segment. The 5'-side thymine base is parallel to the side chain of Tyr100iH of the antibody heavy chain and is also involved in electrostatic interactions with Asn30L, Tyr32L and Lys50L of the antibody light chain. The 5'-side and 3'-side phosphate groups exhibit electrostatic interactions with Asn28L and Ser58H, respectively. These interactions with the flanking nucleotides explain why longer oligonucleotides containing dT(6-4)T segments in the centre show higher antibody-binding affinities than the dT(6-4)T ligand.

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Related Citations: 

• Simultaneous Establishment of Monoclonal Antibodies Specific for Either Cyclobutane Pyrimidine Dimer or (6-4)photoproduct from the Same Mouse Immunized Ultraviolet-irradiated DNA
  Mori, T.,Nakane, M.,Hattori, T.,Matsunaga, T.,Ihara, M.,Nikaido, O.
  (1991) Photochem.Photobiol. 54: 225
• Crystal Structure of the 64M-2 Antibody Fab Fragment in Complex with a DNA dT(6-4)T Photoproduct formed by Ultraviolet Radiation
  Yokoyama, H.,Mizutani, R.,Satow, Y.,Komatsu, Y.,Ohtsuka, E.,Nikaido, O.
  (2000) J.Mol.Biol. 299: 711




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Anti-(6-4) photoproduct antibody 64M-2 Fab (light chain)	L	216	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Anti-(6-4) photoproduct antibody 64M-2 Fab (heavy chain)	H	220	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*TP*(64T)P*TP*T)-3'	A	4	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NI	L	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
64T	A	DNA LINKING	C10 H17 N2 O9 P		DT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 73.567	α = 90.00
b = 137.274	β = 90.00
c = 49.615	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-15 
• Released Date: 2002-11-15 
• Deposition Author(s): Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E., Nikaido, O.

Revision History 

• Version 1.0: 2002-11-15
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2012-02-29
  Type: Database references
• Version 1.4: 2012-03-28
  Type: Database references