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- PDB-4ne5: Human MHF1-MHF2 complex -

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Basic information

Entry
Database: PDB / ID: 4ne5
TitleHuman MHF1-MHF2 complex
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / Histone fold / DNA repair / genome maintenance / Fanconi Anemia / FancM / Nucleus
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 / Resolution: 2.5 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
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
B: Centromere protein X
C: Centromere protein S
D: Centromere protein X
E: Centromere protein S
F: Centromere protein X
G: Centromere protein S
H: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)76,7438
Polymers76,7438
Non-polymers00
Water2,648147
1
A: Centromere protein S
B: Centromere protein X
E: Centromere protein S
F: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)38,3714
Polymers38,3714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-111 kcal/mol
Surface area17050 Å2
MethodPISA
2
C: Centromere protein S
D: Centromere protein X
G: Centromere protein S
H: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)38,3714
Polymers38,3714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-111 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.076, 128.760, 88.836
Angle α, β, γ (deg.)90.000, 100.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 14:106 )
21chain C and (resseq 14:106 )
31chain E and (resseq 14:106 )
41chain G and (resseq 14:106 )
12chain B and (resseq 8:81 )
22chain D and (resseq 8:81 )
32chain F and (resseq 8:81 )
42chain H and (resseq 8:81 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 14:106 )A0
211chain C and (resseq 14:106 )C0
311chain E and (resseq 14:106 )E0
411chain G and (resseq 14:106 )G0
112chain B and (resseq 8:81 )B8 - 81
212chain D and (resseq 8:81 )D8 - 81
312chain F and (resseq 8:81 )F8 - 81
412chain H and (resseq 8:81 )H8 - 81

NCS ensembles :
ID
1
2

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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.: 4
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 2 / 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.: 4
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 2 / References: UniProt: A8MT69
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 300 K / Method: micro-batch under oil / Details: Micro-batch under oil, temperature 300K / PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / 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: 2.5→38.51 Å / Num. all: 31370 / Num. obs: 31307 / % possible obs: 99.8 % / 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: 2.5→38.51 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8095 / SU ML: 0.37 / σ(F): 0 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1575 5.03 %
Rwork0.2295 --
obs0.2312 31307 99.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.593 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 113.85 Å2 / Biso mean: 45.3681 Å2 / Biso min: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.9765 Å2-0 Å22.7228 Å2
2---0.7593 Å20 Å2
3----0.2172 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 0 147 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085388
X-RAY DIFFRACTIONf_angle_d0.9887232
X-RAY DIFFRACTIONf_chiral_restr0.072856
X-RAY DIFFRACTIONf_plane_restr0.003920
X-RAY DIFFRACTIONf_dihedral_angle_d15.6632048
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A743X-RAY DIFFRACTIONPOSITIONAL0.047
12C743X-RAY DIFFRACTIONPOSITIONAL0.047
13E743X-RAY DIFFRACTIONPOSITIONAL0.077
14G743X-RAY DIFFRACTIONPOSITIONAL0.078
21B590X-RAY DIFFRACTIONPOSITIONAL0.043
22D590X-RAY DIFFRACTIONPOSITIONAL0.043
23F590X-RAY DIFFRACTIONPOSITIONAL0.049
24H590X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58070.35571310.31962712284399
2.5807-2.67290.31731310.294726702801100
2.6729-2.77990.30231230.283927312854100
2.7799-2.90640.32831580.266926752833100
2.9064-3.05950.3031560.271326842840100
3.0595-3.25110.28881490.243226842833100
3.2511-3.5020.24551450.232527052850100
3.502-3.85410.24231520.219126992851100
3.8541-4.41110.25321490.20626892838100
4.4111-5.55490.22071370.191627402877100
5.5549-38.51410.23771440.201627432887100

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