+Open data
-Basic information
Entry | Database: PDB / ID: 4drb | ||||||
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Title | The crystal structure of FANCM bound MHF complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/PROTEIN BINDING / DNA repair / DNA binding complex / Histone fold / DNA damage repair / DNA binding / DNA BINDING-PROTEIN BINDING complex / DNA BINDING PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information FANCM-MHF complex / double-strand break repair via synthesis-dependent strand annealing / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / four-way junction helicase activity / nuclease activity / kinetochore assembly / inner kinetochore / positive regulation of protein monoubiquitination / replication fork processing ...FANCM-MHF complex / double-strand break repair via synthesis-dependent strand annealing / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / four-way junction helicase activity / nuclease activity / kinetochore assembly / inner kinetochore / positive regulation of protein monoubiquitination / replication fork processing / 3'-5' DNA helicase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / four-way junction DNA binding / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / positive regulation of protein ubiquitination / chromosome segregation / RHO GTPases Activate Formins / Fanconi Anemia Pathway / PKR-mediated signaling / Separation of Sister Chromatids / RNA helicase activity / RNA helicase / protein heterodimerization activity / cell division / DNA repair / DNA damage response / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.634 Å | ||||||
Authors | Tao, Y. / Niu, L. / Teng, M. | ||||||
Citation | Journal: Nat Commun / Year: 2012 Title: The structure of the FANCM-MHF complex reveals physical features for functional assembly Authors: Tao, Y. / Jin, C. / Li, X. / Qi, S. / Chu, L. / Niu, L. / Yao, X. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4drb.cif.gz | 268.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4drb.ent.gz | 222.9 KB | Display | PDB format |
PDBx/mmJSON format | 4drb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4drb_validation.pdf.gz | 540.2 KB | Display | wwPDB validaton report |
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Full document | 4drb_full_validation.pdf.gz | 569.5 KB | Display | |
Data in XML | 4drb_validation.xml.gz | 47.5 KB | Display | |
Data in CIF | 4drb_validation.cif.gz | 66.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/4drb ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4drb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14325.699 Da / Num. of mol.: 6 / Fragment: C-terminus deleted, UNP residues 1-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APITD1, CENPS, FAAP16, MHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N2Z9 #2: Protein | Mass: 16845.693 Da / Num. of mol.: 3 / Fragment: MHF binding domain, UNP residues 661-800 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYD8 #3: Protein | Mass: 9348.481 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STRA13, CENPX, FAAP10, MHF2 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MT69 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, pH 8.5, 0.2 M (NH4)2SO4, 25% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.634→50 Å / Num. obs: 52925 / % possible obs: 100 % / Biso Wilson estimate: 40.36 Å2 |
Reflection shell | Resolution: 2.634→2.73 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.62 / Num. unique all: 5221 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.634→49.67 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8165 / SU ML: 0.35 / σ(F): 0 / Phase error: 25.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.932 Å2 / ksol: 0.301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.71 Å2 / Biso mean: 44.9905 Å2 / Biso min: 14.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.634→49.67 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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