+Open data
-Basic information
Entry | Database: PDB / ID: 7ldg | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the MEILB2-BRCA2 complex | ||||||||||||
Components |
| ||||||||||||
Keywords | RECOMBINATION / Complex / Recruiter / Protein-protein interaction / Armadillo-repeat | ||||||||||||
Function / homology | Function and homology information BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element / telomere maintenance via recombination / regulation of DNA damage checkpoint / oocyte maturation / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA repair complex / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / female meiosis I / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / double-strand break repair / cellular senescence / single-stranded DNA binding / chromosome / spermatogenesis / protease binding / transcription by RNA polymerase II / chromosome, telomeric region / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.56 Å | ||||||||||||
Authors | Nandakumar, J. / Pendlebury, D.F. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2021 Title: Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites. Authors: Pendlebury, D.F. / Zhang, J. / Agrawal, R. / Shibuya, H. / Nandakumar, J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ldg.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ldg.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ldg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/7ldg ftp://data.pdbj.org/pub/pdb/validation_reports/ld/7ldg | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28304.908 Da / Num. of mol.: 2 / Fragment: aa83-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSF2BP, MEILB2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75031 #2: Protein | Mass: 7738.730 Da / Num. of mol.: 2 / Fragment: MEILB2-binding domain (aa2271-2335) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2, FACD, FANCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51587 #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.22 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate (pH 4.6), 2 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97895 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97895 Å / Relative weight: 1 |
Reflection | Resolution: 2.56→89.94 Å / Num. obs: 35987 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.56→2.7 Å / Redundancy: 21.7 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 2 / Num. unique obs: 5188 / CC1/2: 0.833 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.56→31.1 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.72 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.56→31.1 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.56→2.63 Å
|