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Contents |
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* Residue conservation analysis
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PDB id:
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Gene regulation/antitumor protein/DNA
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Title:
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Structure of a brca2-dss1-ssdna complex
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Structure:
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5'-d(p Tp Tp Tp Tp Tp T)-3'. Chain: c. Engineered: yes. Deleted in split hand/split foot protein 1. Chain: b. Synonym: dss1, split hand/foot deleted protein 1. Engineered: yes. Breast cancer 2. Chain: a.
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Source:
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Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Mus musculus. House mouse. Organism_taxid: 10090.
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Biol. unit:
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Hexamer (from
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Resolution:
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3.50Å
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R-factor:
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0.245
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R-free:
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0.278
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Authors:
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H.Yang,P.D.Jeffrey,J.Miller,E.Kinnucan,Y.Sun,N.H.Thoma,N.Zheng, P.L.Chen,W.H.Lee,N.P.Pavletich
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Key ref:
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H.Yang
et al.
(2002).
BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.
Science,
297,
1837-1848.
PubMed id:
DOI:
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Date:
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27-Aug-02
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Release date:
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27-Sep-02
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PROCHECK
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Headers
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References
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DOI no:
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Science
297:1837-1848
(2002)
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PubMed id:
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BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.
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H.Yang,
P.D.Jeffrey,
J.Miller,
E.Kinnucan,
Y.Sun,
N.H.Thoma,
N.Zheng,
P.L.Chen,
W.H.Lee,
N.P.Pavletich.
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ABSTRACT
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Mutations in the BRCA2 (breast cancer susceptibility gene 2) tumor suppressor
lead to chromosomal instability due to defects in the repair of double-strand
DNA breaks (DSBs) by homologous recombination, but BRCA2's role in this process
has been unclear. Here, we present the 3.1 angstrom crystal structure of a
approximately 90-kilodalton BRCA2 domain bound to DSS1, which reveals three
oligonucleotide-binding (OB) folds and a helix-turn-helix (HTH) motif. We also
(i) demonstrate that this BRCA2 domain binds single-stranded DNA, (ii) present
its 3.5 angstrom structure bound to oligo(dT)9, (iii) provide data that
implicate the HTH motif in dsDNA binding, and (iv) show that BRCA2 stimulates
RAD51-mediated recombination in vitro. These findings establish that BRCA2
functions directly in homologous recombination and provide a structural and
biochemical basis for understanding the loss of recombination-mediated DSB
repair in BRCA2-associated cancers.
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Selected figure(s)
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Figure 3.
Fig. 3. DSS1 binds BRCA2 in an extended conformation,
interacting with basic grooves on the helical domain, OB1 and
OB2 domains. (A) The NH[2]-terminal segment of DSS1 (orange)
tunnels through the helical domain (magenta), and also contacts
OB1 (green). View is rotated ~180° about the horizontal axis
relative to Fig. 1D. In addition to the contacts discussed in
the text, Glu14 of DSS1 interacts with Lys2712 of OB1, Glu15
with Gln2576, Asp16 with Lys2671, Asp17 with Lys2551, and Glu18
with Lys2435 and Arg2441. In addition, Asp16 forms a salt bridge
with Arg57, located on the COOH-terminal DSS1 segment that binds
on the opposite side of BRCA2. (B) Surface representation of the
helical domain-OB1 region that binds the NH[2]-terminal segment
of DSS1, in an orientation similar to that of (A). The surface
is colored according to the electrostatic potential (-30 kT to
+30 kT), calculated in the absence of DSS1 with the program
GRASP (92). The backbone traces of the NH[2]-terminal and part
of the COOH-terminal DSS1 segments are shown as white coils, and
the side chains, in yellow. The white-dotted line indicates the
11-residue disordered segment between the NH[2]- and
COOH-terminal segments of DSS1. DSS1 residues that are entirely
buried below the surface of BRCA2 are indicated in parenthesis.
The side chains for residues 46 to 49 of the COOH-terminal
segment have poor electron density and are omitted. (C) Surface
representation of the helical domain-OB1-OB2 region that binds
the COOH-terminal segment of DSS1, in an orientation rotated
~90° about the vertical axis relative to (B). Hydrophobic
interactions include the DSS1 Phe^19, Trp39, Trp43, which pack
with Trp2646, Phe^2722, and with an opening in the hydrophobic
core of OB1, respectively. In addition, the majority of the
acidic DSS1 residues are near clusters of basic BRCA2 residues.
These include Glu40, Asp41, and Asp44, which are near Arg2708,
Lys2898, and Lys2655; Asp50 and Asp51, which are near Arg2708
and Arg2451; and Glu20 and Glu21 [from the NH[2]-terminal
segment in (B)] which are near Lys2712, Arg2717, Arg2590 and
Lys2595.
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Figure 4.
Fig. 4. BRCA2 contains a three-helix bundle (3HB) similar to
the helix-turn-helix dsDNA binding motif. The 35-residue BRCA2
3HB is superimposed on the 36-residue 3HB domain of the Hin
recombinase DNA binding domain (48). The 35 residues correspond
to the entire 3HB, starting with the NH[2]-terminus of T  2 and
ending at the COOH-terminus of T 4. There
is only one residue insertion between H2 and H3 of the Hin
recombinase 3HB in the alignment.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
297,
1837-1848)
copyright 2002.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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R.Roy,
J.Chun,
and
S.N.Powell
(2012).
BRCA1 and BRCA2: different roles in a common pathway of genome protection.
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Nat Rev Cancer,
12,
68-78.
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|
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A.Bazzi,
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C.Boudier,
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P.Fossé,
and
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(2011).
Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC.
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Nucleic Acids Res,
39,
3903-3916.
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PDB code:
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A.Shibata,
S.Conrad,
J.Birraux,
V.Geuting,
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and
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Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53.
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Structure,
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M.Hall,
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Peptide aptamer mimicking RAD51-binding domain of BRCA2 inhibits DNA damage repair and survival in Trypanosoma brucei.
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Mutational analysis of Brh2 reveals requirements for compensating mediator functions.
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A new mutation of BRCA2 gene in an Italian healthy woman with familial breast cancer history.
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Structures of a key interaction protein from the Trypanosoma brucei editosome in complex with single domain antibodies.
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J Struct Biol,
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PDB codes:
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|
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W.K.Holloman
(2011).
Unraveling the mechanism of BRCA2 in homologous recombination.
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J.Liu,
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Human BRCA2 protein promotes RAD51 filament formation on RPA-covered single-stranded DNA.
|
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|
| |
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A.Carreira,
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Purified human BRCA2 stimulates RAD51-mediated recombination.
|
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| |
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| |
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PDB code:
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|
|
|
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Y.Takizawa,
Y.Qing,
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|
| |
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| |
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The BRC repeats of human BRCA2 differentially regulate RAD51 binding on single- versus double-stranded DNA to stimulate strand exchange.
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| |
Proc Natl Acad Sci U S A,
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Template-based recognition of protein fold within the midnight and twilight zones of protein sequence similarity.
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Mediating repair.
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Nat Struct Mol Biol,
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Cancer: catalyst of a catalyst.
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Nature,
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From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold.
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Curr Opin Struct Biol,
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BRCA2 is ubiquitinated in vivo and interacts with USP11, a deubiquitinating enzyme that exhibits prosurvival function in the cellular response to DNA damage.
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Mol Cell Biol,
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Annu Rev Biochem,
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Cell cycle localization, dimerization, and binding domain architecture of the telomere protein cPot1.
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Mol Cell Biol,
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Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2.
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Am J Hum Genet,
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D.J.Richard,
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Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase.
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Nucleic Acids Res,
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(2004).
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
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Nat Struct Mol Biol,
11,
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PDB codes:
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|
|
|
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|
J.H.Eastberg,
J.Pelletier,
and
B.L.Stoddard
(2004).
Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
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Nucleic Acids Res,
32,
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PDB codes:
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J.M.Stark,
A.J.Pierce,
J.Oh,
A.Pastink,
and
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Genetic steps of mammalian homologous repair with distinct mutagenic consequences.
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Mol Cell Biol,
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BRCA2 in meiosis: turning over a new leaf.
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Trends Cell Biol,
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C.J.Lord,
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A.N.Tutt,
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(2004).
DSS1 is required for RAD51 focus formation and genomic stability in mammalian cells.
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EMBO Rep,
5,
989-993.
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M.Lei,
E.R.Podell,
and
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Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection.
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Nat Struct Mol Biol,
11,
1223-1229.
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PDB code:
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|
N.J.Krogan,
M.H.Lam,
J.Fillingham,
M.C.Keogh,
M.Gebbia,
J.Li,
N.Datta,
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S.Buratowski,
A.Emili,
and
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(2004).
Proteasome involvement in the repair of DNA double-strand breaks.
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Mol Cell,
16,
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E.Dray,
I.Gy,
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Brca2 is involved in meiosis in Arabidopsis thaliana as suggested by its interaction with Dmc1.
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EMBO J,
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S.L.Arcand,
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D.M.Provencher,
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(2004).
Chemosensitivity and radiosensitivity profiles of four new human epithelial ovarian cancer cell lines exhibiting genetic alterations in BRCA2, TGFbeta-RII, KRAS2, TP53 and/or CDNK2A.
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Cancer Chemother Pharmacol,
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and
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Recombination mechanisms; fortieth anniversary meeting of the Holliday model.
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Mol Cell,
16,
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X.Wang,
P.R.Andreassen,
and
A.D.D'Andrea
(2004).
Functional interaction of monoubiquitinated FANCD2 and BRCA2/FANCD1 in chromatin.
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Mol Cell Biol,
24,
5850-5862.
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A.D.D'Andrea,
and
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(2003).
The Fanconi anaemia/BRCA pathway.
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Nat Rev Cancer,
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S.Sechi,
M.Wallisch,
D.Yang,
M.K.Young,
H.Joenje,
M.E.Hoatlin,
and
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A multiprotein nuclear complex connects Fanconi anemia and Bloom syndrome.
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Mol Cell Biol,
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A.Waterworth
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New insights into the biological function of BRCA2 from its structural interactions.
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Breast Cancer Res,
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Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.
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EMBO J,
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PDB codes:
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|
|
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|
D.S.Shin,
L.Pellegrini,
D.S.Daniels,
B.Yelent,
L.Craig,
D.Bates,
D.S.Yu,
M.K.Shivji,
C.Hitomi,
A.S.Arvai,
N.Volkmann,
H.Tsuruta,
T.L.Blundell,
A.R.Venkitaraman,
and
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(2003).
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.
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EMBO J,
22,
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PDB code:
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I.Cass,
R.L.Baldwin,
T.Varkey,
R.Moslehi,
S.A.Narod,
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Improved survival in women with BRCA-associated ovarian carcinoma.
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Cancer,
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Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein.
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EMBO J,
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PDB code:
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K.Yamamoto,
M.Ishiai,
N.Matsushita,
H.Arakawa,
J.E.Lamerdin,
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Fanconi anemia FANCG protein in mitigating radiation- and enzyme-induced DNA double-strand breaks by homologous recombination in vertebrate cells.
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The BRCA2-interacting protein DSS1 is vital for DNA repair, recombination, and genome stability in Ustilago maydis.
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Mol Cell,
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Functional inactivation of the conserved Sem1p in yeast by intrabodies.
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Yeast,
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Ontologies for proteomics: towards a systematic definition of structure and function that scales to the genome level.
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Molecular views of recombination proteins and their control.
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Epithelial cancer in Fanconi anemia complementation group D2 (Fancd2) knockout mice.
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Characterization of Arabidopsis thaliana ortholog of the human breast cancer susceptibility gene 1: AtBRCA1, strongly induced by gamma rays.
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Deep trefoil knot implicated in RNA binding found in an archaebacterial protein.
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PDB code:
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|
Y.Shiloh
(2003).
ATM and related protein kinases: safeguarding genome integrity.
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BRCA2 keeps Rad51 in line. High-fidelity homologous recombination prevents breast and ovarian cancer?
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Mol Cell,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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 |
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