PDBsum entry 3vw3

Immune system/DNA

PDB id: 3vw3

Contents

Protein chains

215 a.a.

216 a.a.

DNA/RNA

Ligands

NCO

Waters ×144

PDB id:

3vw3

Name:

Immune system/DNA

Title:

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

Structure:

Anti-(6-4) photoproduct antibody 64m-5 fab (light chain). Chain: l. Anti-(6-4) photoproduct antibody 64m-5 fab (heavy chain). Chain: h. DNA (5'-d( Gp Cp Gp Ap Gp Tp Gp Ap (64T)p (5Py) p Ap Tp Gp Gp Ap Cp Gp G)-3'). Chain: a. Engineered: yes. DNA (5'-

Source:

Mus musculus. Organism_taxid: 10090. Strain: balb/c. Other_details: hybridoma. Synthetic: yes. Other_details: DNA with (6-4) photoproduct. Other_details: synthetic DNA

Resolution:

2.50Å R-factor: 0.247 R-free: 0.290

Authors:

H.Yokoyama,R.Mizutani,Y.Satow

Key ref:

H.Yokoyama et al. (2013). Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab. Acta Crystallogr D Biol Crystallogr, 69, 504-512. PubMed id: 23519658 DOI: 10.1107/S0907444912050007

Date:

30-Jul-12 Release date: 27-Mar-13

Protein chain

No UniProt id for this chain

Struc: 215 a.a.

Protein chain

No UniProt id for this chain

Struc: 216 a.a.

DNA/RNA chains

G-C-G-A-G-T-G-A-64T-5PY-A-T-G-G-A-C-G-G 18 bases

C-C-C-G-T-C-C-A-T-A-A-T-C-A-C-T-C-G 18 bases

DOI no: 10.1107/S0907444912050007

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

PubMed id: 23519658

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

H.Yokoyama, R.Mizutani, Y.Satow.

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.