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- PDB-4e45: Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Com... -

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Basic information

Entry
Database: PDB / ID: 4.0E+45
TitleCrystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Complex with Fanconi Anemia Associated Helicase hFANCM
Components
  • (Centromere protein ...) x 2
  • Fanconi anemia group M protein
KeywordsDNA BINDING PROTEIN/HYDROLASE / Histone-Fold / Pentamer / Fanconi Anemia / Helicase / FANCM / MHF / DNA BINDING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / four-way junction helicase activity / nuclease activity / kinetochore assembly / 3'-5' DNA helicase activity / positive regulation of protein monoubiquitination ...double-strand break repair via synthesis-dependent strand annealing / FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / four-way junction helicase activity / nuclease activity / kinetochore assembly / 3'-5' DNA helicase activity / positive regulation of protein monoubiquitination / replication fork processing / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / Mitotic Prometaphase / four-way junction DNA binding / 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
FANCM, DEAH-box helicase domain / : / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM to MHF binding domain / 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 ...FANCM, DEAH-box helicase domain / : / Fanconi anemia group M protein, MHF binding domain / FANCM/Mph1-like / FANCM to MHF binding domain / 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 / ERCC4 domain / ERCC4 domain / ERCC4 domain / RuvA domain 2-like / Restriction endonuclease type II-like / Histone, subunit A / Histone, subunit A / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Helicase conserved C-terminal domain / Special / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere protein X / Fanconi anemia group M protein / Centromere protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centromere protein S
B: Centromere protein X
C: Centromere protein S
D: Centromere protein X
E: Fanconi anemia group M protein
F: Centromere protein S
G: Centromere protein X
H: Centromere protein S
I: Centromere protein X
J: Fanconi anemia group M protein
K: Centromere protein S
L: Centromere protein X
M: Centromere protein S
N: Centromere protein X
O: Fanconi anemia group M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,33520
Polymers181,95515
Non-polymers3805
Water9,836546
1
A: Centromere protein S
B: Centromere protein X
C: Centromere protein S
D: Centromere protein X
E: Fanconi anemia group M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8097
Polymers60,6525
Non-polymers1582
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19190 Å2
ΔGint-161 kcal/mol
Surface area19080 Å2
MethodPISA
2
F: Centromere protein S
G: Centromere protein X
H: Centromere protein S
I: Centromere protein X
J: Fanconi anemia group M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8097
Polymers60,6525
Non-polymers1582
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19010 Å2
ΔGint-166 kcal/mol
Surface area19170 Å2
MethodPISA
3
K: Centromere protein S
L: Centromere protein X
M: Centromere protein S
N: Centromere protein X
O: Fanconi anemia group M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7176
Polymers60,6525
Non-polymers651
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-155 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.980, 69.970, 116.050
Angle α, β, γ (deg.)90.000, 91.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Centromere protein ... , 2 types, 12 molecules ACFHKMBDGILN

#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.: 6 / 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.: 6
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

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Protein , 1 types, 3 molecules EJO

#3: Protein Fanconi anemia group M protein / Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa ...Protein FACM / ATP-dependent RNA helicase FANCM / Fanconi anemia-associated polypeptide of 250 kDa / FAAP250 / Protein Hef ortholog


Mass: 16333.175 Da / Num. of mol.: 3 / Fragment: UNP residues 667-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FANCM, KIAA1596 / Plasmid: parallel MBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IYD8, RNA helicase

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Non-polymers , 3 types, 551 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
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→49.51 Å / Num. all: 120454 / Num. obs: 119106 / % possible obs: 98.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 40.705 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.512331654886499.7
2.05-2.110.3943.930710859799.7
2.11-2.170.3529792834099.7
2.17-2.240.2376.229111815599.8
2.24-2.310.1897.428214788799.8
2.31-2.390.15927349764699.9
2.39-2.480.1210.626461738599.8
2.48-2.580.09912.525493712799.7
2.58-2.70.07914.824271679299.7
2.7-2.830.06716.723218650299.6
2.83-2.980.05519.422042618799.4
2.98-3.160.04722.420790585499.5
3.16-3.380.04125.119464551399.4
3.38-3.650.03728.118071514199.4
3.65-40.03529.816384469598.9
4-4.470.0343114728425898.6
4.47-5.160.03331.312819375098
5.16-6.320.03530.510965321298.6
6.32-8.940.035317634232991.8
8.940.03329.3249487260.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.47 Å
Translation2.5 Å43.47 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→49.51 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.298 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5972 5 %RANDOM
Rwork0.202 ---
all0.202 120454 --
obs0.204 119090 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.212 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20.16 Å2
2--1.31 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 2→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10421 0 15 546 10982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910655
X-RAY DIFFRACTIONr_bond_other_d0.0020.027086
X-RAY DIFFRACTIONr_angle_refined_deg1.521.95514399
X-RAY DIFFRACTIONr_angle_other_deg0.952317223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.251331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53123.752501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.157151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5541583
X-RAY DIFFRACTIONr_chiral_restr0.0930.21682
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022242
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 417 -
Rwork0.286 8194 -
all-8611 -
obs--99.57 %

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