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- PDB-4dra: Crystal structure of MHF complex -

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Basic information

Entry
Database: PDB / ID: 4dra
TitleCrystal structure of MHF complex
Components
  • Centromere protein S
  • Centromere protein X
KeywordsDNA BINDING PROTEIN / DNA binding complex / DNA damage repair / Histone-fold
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: 2.414 Å
AuthorsTao, Y. / Niu, L. / Teng, M.
CitationJournal: 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
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: Centromere protein S
C: Centromere protein S
D: Centromere protein S
E: Centromere protein X
F: Centromere protein X
G: Centromere protein X
H: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)90,3318
Polymers90,3318
Non-polymers00
Water2,090116
1
A: Centromere protein S
D: Centromere protein S
E: Centromere protein X
H: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)45,1654
Polymers45,1654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-103 kcal/mol
Surface area16200 Å2
MethodPISA
2
B: Centromere protein S
C: Centromere protein S
F: Centromere protein X
G: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)45,1654
Polymers45,1654
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-104 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.007, 128.771, 88.697
Angle α, β, γ (deg.)90.00, 100.74, 90.00
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: 13327.983 Da / Num. of mol.: 4 / Fragment: C-terminus deleted, UNP residues 1-107
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
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: 9254.691 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) / References: UniProt: A8MT69
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M HEPES-NaOH, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 32631 / % possible obs: 94.1 %
Reflection shellResolution: 2.41→2.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.53 / Num. unique all: 1477 / % possible all: 86.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.414→34.153 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8237 / SU ML: 0.34 / σ(F): 0.1 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 1592 5.08 %
Rwork0.1904 --
obs0.193 31356 90.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.417 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 143.5 Å2 / Biso mean: 44.7119 Å2 / Biso min: 9.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.1987 Å2-0 Å26.3156 Å2
2--3.6898 Å20 Å2
3----1.491 Å2
Refinement stepCycle: LAST / Resolution: 2.414→34.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5227 0 0 116 5343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035335
X-RAY DIFFRACTIONf_angle_d0.5577203
X-RAY DIFFRACTIONf_dihedral_angle_d18.7231932
X-RAY DIFFRACTIONf_chiral_restr0.038868
X-RAY DIFFRACTIONf_plane_restr0.001924
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4136-2.49980.30981250.2372240774
2.4998-2.59990.33561500.2232266081
2.5999-2.71810.29281510.2164276584
2.7181-2.86140.2581350.214286587
2.8614-3.04050.28311710.2157288889
3.0405-3.27510.24311610.2075306593
3.2751-3.60440.26661680.1895321097
3.6044-4.12520.21591600.1767332199
4.1252-5.19440.20261780.1567328099
5.1944-34.15660.19921930.1708330399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1253-0.0583-1.05720.4701-0.49622.0141-0.3607-0.0615-0.09920.1223-0.0181-0.03970.4204-0.1619-0.00020.34290.00680.05620.1791-0.03380.17987.171-16.310649.5468
20.58720.45180.18481.17390.35611.10530.01880.1341-0.0702-0.0692-0.0944-0.0271-0.00410.0361-00.21820.04530.02720.15910.00490.1462-12.58-27.329-9.1951
31.53590.30520.58561.3246-0.5231.27590.0204-0.0855-0.15680.05290.0443-0.1231-0.0993-0.1024-00.04070.0025-0.01180.11880.02660.1112-8.142-35.922417.6915
41.1028-0.5519-0.38631.12520.16380.76620.01290.17840.0811-0.047-0.00040.07550.0652-0.105800.0496-0.0052-0.02490.13070.02750.122910.26140.249826.5708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D'
2X-RAY DIFFRACTION2chain 'C'
3X-RAY DIFFRACTION3chain 'B'
4X-RAY DIFFRACTION4chain 'A'

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