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- PDB-4e44: Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer -

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Basic information

Entry
Database: PDB / ID: 4.0E+44
TitleCrystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / Histone-Fold / Tetramer / Fanconi Anemia / FANCM / MHF
Function / homology
Function and homology information


FANCM-MHF complex / Fanconi anaemia nuclear complex / resolution of meiotic recombination intermediates / kinetochore assembly / inner kinetochore / 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 / resolution of meiotic recombination intermediates / kinetochore assembly / inner kinetochore / 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 / molecular replacement / Resolution: 2.1 Å
AuthorsFox III, D. / Zhao, Y. / Yang, W. / Weidong, W.
CitationJournal: To be Published
Title: Crystal Structures Reveal that FANCM remodels the MHF Tetramer in favor of binding Branched DNA
Authors: Fox III, D. / Yan, Z. / Ling, C. / Zhao, Y. / Lee, D.Y. / Yang, W. / Weidong, W.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3184
Polymers44,3184
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10670 Å2
ΔGint-110 kcal/mol
Surface area17820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.780, 91.930, 61.430
Angle α, β, γ (deg.)90.000, 96.300, 90.000
Int Tables number4
Space group name H-MP1211

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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: 13042.696 Da / Num. of mol.: 2 / Fragment: UNP residues 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APITD1, CENPS, FAAP16, MHF1 / Plasmid: pGEX/pHis bicistronic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 9116.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STRA13, CENPX, FAAP10, MHF2 / Plasmid: pGEX/pHis bicistronic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8MT69
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Tracking Code C4, 0.1M Tris pH 7.8, 0.2M LiCl, 0.1M Na2SO4, 17.5% w/v PEG3350, 10% glycerol cryo., vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.1→45.97 Å / Num. all: 26336 / Num. obs: 25440 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 40.09 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.5483.55262187196.9
2.15-2.210.4484.15146183398
2.21-2.280.3315.35091181497.3
2.28-2.350.2985.74886173897.8
2.35-2.420.2416.74795168996.7
2.42-2.510.1977.84584162998
2.51-2.60.1488.94399155096.9
2.6-2.710.12210.24309153497.6
2.71-2.830.10211.74084144196.6
2.83-2.970.0813.23937139497
2.97-3.130.06515.43735133097.1
3.13-3.320.05517.23437122695.8
3.32-3.550.04918.83165114395.4
3.55-3.830.04520.23013110696.6
3.83-4.20.04320.9266698795.5
4.2-4.70.03722.1250291697.4
4.7-5.420.03821.9224281596.9
5.42-6.640.03621.8185768095.6
6.64-9.390.03322.6140851193.2
9.390.03222.359823372.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.53 Å
Translation2.5 Å30.53 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TAF

1taf


Resolution: 2.1→45.97 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.641 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1278 5 %RANDOM
Rwork0.2 ---
all0.2 26336 --
obs0.201 25419 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20.19 Å2
2--1.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 0 97 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192717
X-RAY DIFFRACTIONr_bond_other_d0.0010.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9643669
X-RAY DIFFRACTIONr_angle_other_deg1.01734364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3495349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65824.215121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21915478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.131519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 91 -
Rwork0.236 1737 -
all-1828 -
obs--96.87 %

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