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Yorodumi- PDB-7k3s: Solution NMR Structure of the Coiled-coil BRCA1-PALB2 Heterodimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k3s | ||||||||||||
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Title | Solution NMR Structure of the Coiled-coil BRCA1-PALB2 Heterodimer | ||||||||||||
Components |
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Keywords | ONCOPROTEIN / Homologous Recombination / DNA | ||||||||||||
Function / homology | Function and homology information : / : / : / : / : / : / : / mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / Homologous DNA Pairing and Strand Exchange ...: / : / : / : / : / : / : / mitotic G2 DNA damage checkpoint signaling => GO:0007095 / : / Homologous DNA Pairing and Strand Exchange / : / regulation of cell cycle => GO:0051726 / Resolution of D-loop Structures through Holliday Junction Intermediates / : / SUMOylation of DNA damage response and repair proteins / HDR through Homologous Recombination (HRR) / BRCA1-BARD1 complex / BRCA1-A complex / negative regulation of intracellular estrogen receptor signaling pathway / : / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / lateral element / dosage compensation by inactivation of X chromosome / protein K6-linked ubiquitination / post-anal tail morphogenesis / mitotic G2/M transition checkpoint / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / inner cell mass cell proliferation / response to ionizing radiation / mesoderm development / centrosome duplication / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / embryonic organ development / somitogenesis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / condensed chromosome / positive regulation of DNA repair / condensed nuclear chromosome / positive regulation of protein ubiquitination / chromosome segregation / animal organ morphogenesis / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / multicellular organism growth / fatty acid biosynthetic process / positive regulation of protein import into nucleus / response to estrogen / positive regulation of angiogenesis / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / cellular response to tumor necrosis factor / chromosome / in utero embryonic development / damaged DNA binding / transcription coactivator activity / nuclear body / transcription cis-regulatory region binding / protein ubiquitination / mitochondrial matrix / ribonucleoprotein complex / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / DNA damage response / chromatin binding / apoptotic process / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | SOLUTION NMR / simulated annealing | ||||||||||||
Authors | Daigham, N.S. / Liu, G. / Bunting, S.F. / Montelione, G.T. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: The Structural Basis for Interactions Between PALB2 and BRCA1 that Mediate the Homologous Recombination DNA Damage Repair Process Authors: Daigham, N.S. / Liu, G. / Bunting, S.F. / Montelione, G.T. #1: Journal: Biochemistry / Year: 2018 Title: Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2. Authors: Song, F. / Li, M. / Liu, G. / Swapna, G.V.T. / Daigham, N.S. / Xia, B. / Montelione, G.T. / Bunting, S.F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k3s.cif.gz | 703.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k3s.ent.gz | 598.9 KB | Display | PDB format |
PDBx/mmJSON format | 7k3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k3s_validation.pdf.gz | 543.1 KB | Display | wwPDB validaton report |
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Full document | 7k3s_full_validation.pdf.gz | 739.3 KB | Display | |
Data in XML | 7k3s_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 7k3s_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/7k3s ftp://data.pdbj.org/pub/pdb/validation_reports/k3/7k3s | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6935.690 Da / Num. of mol.: 1 / Fragment: residues 1337-1387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Gene: Brca1 / Plasmid: MmR494A-1337-1387 / Production host: Escherichia coli (E. coli) References: UniProt: P48754, RING-type E3 ubiquitin transferase |
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#2: Protein | Mass: 7948.166 Da / Num. of mol.: 1 / Fragment: residues 1-60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Palb2 / Plasmid: MmR495A-1-60 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q3U0P1 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: Buffer Conditions: 20 mM MES, 200 mM NaCl, 10 mM DTT, 5 mM CaCl2 at pH 6.5 Ionic strength: 200 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 7 / Details: molecular dynamics | |||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 15 |