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- PDB-4ne3: Human MHF1-MHF2 complex -

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Basic information

Entry
Database: PDB / ID: 4ne3
TitleHuman MHF1-MHF2 complex
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / Histone fold / DNA repair / genome maintenance / Fanconi Anemia / FancM
Function / homology
Function and homology information


FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / 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 / protein heterodimerization activity / cell division / DNA repair / DNA damage response / chromatin binding / chromatin / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...GTP Cyclohydrolase I; Chain A, domain 1 - #30 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4980 / GTP Cyclohydrolase I; Chain A, domain 1 / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone, subunit A / Histone, subunit A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Histone-fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein X / Centromere protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8007 Å
AuthorsZhao, Q. / Saro, D. / Sachpatzidis, A. / Sung, P. / Xiong, Y.
CitationJournal: Nat Commun / Year: 2014
Title: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes.
Authors: Zhao, Q. / Saro, D. / Sachpatzidis, A. / Singh, T.R. / Schlingman, D. / Zheng, X.F. / Mack, A. / Tsai, M.S. / Mochrie, S. / Regan, L. / Meetei, A.R. / Sung, P. / Xiong, Y.
History
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centromere protein S
B: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)19,1862
Polymers19,1862
Non-polymers00
Water1,00956
1
A: Centromere protein S
B: Centromere protein X

A: Centromere protein S
B: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)38,3714
Polymers38,3714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10400 Å2
ΔGint-107 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.969, 52.945, 60.283
Angle α, β, γ (deg.)90.000, 114.910, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: Protein Centromere protein S / / CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold ...CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold protein 1 / Fanconi anemia-associated polypeptide of 16 kDa


Mass: 10739.987 Da / Num. of mol.: 1
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) / Strain (production host): BL21 Rossetta / References: UniProt: Q8N2Z9
#2: Protein Centromere protein X / / CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa ...CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa / Retinoic acid-inducible gene D9 protein homolog / Stimulated by retinoic acid gene 13 protein homolog


Mass: 8445.690 Da / Num. of mol.: 1
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) / Strain (production host): BL21 Rossetta / References: UniProt: A8MT69
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.38 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8007→28.102 Å / Num. all: 16522 / Num. obs: 16358 / % possible obs: 99.01 % / Observed criterion σ(F): 0

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8007→28.102 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8007 / SU ML: 0.24 / σ(F): 0 / Phase error: 27.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 826 5.05 %RANDOM
Rwork0.2313 ---
obs0.2324 16358 99.01 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.375 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 92.75 Å2 / Biso mean: 39.9791 Å2 / Biso min: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1-7.9043 Å2-0 Å22.1373 Å2
2---0.9802 Å20 Å2
3----6.9242 Å2
Refinement stepCycle: LAST / Resolution: 1.8007→28.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 0 56 1383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071341
X-RAY DIFFRACTIONf_angle_d0.9281801
X-RAY DIFFRACTIONf_chiral_restr0.063214
X-RAY DIFFRACTIONf_plane_restr0.003229
X-RAY DIFFRACTIONf_dihedral_angle_d13.085507
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8007-1.91350.37731330.32642579271299
1.9135-2.06120.33551630.268825792742100
2.0612-2.26860.26311290.232225972726100
2.2686-2.59670.23951400.213725882728100
2.5967-3.27070.27221310.21852592272399
3.2707-28.10540.22281300.22822597272797

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