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- PDB-7dpd: Human MCM9 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7dpd
TitleHuman MCM9 N-terminal domain
ComponentsDNA helicase MCM9
KeywordsDNA BINDING PROTEIN / Zinc Finger / DNA binding
Function / homology
Function and homology information


MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / female gamete generation / MCM complex / DNA duplex unwinding / protein localization to chromatin ...MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / female gamete generation / MCM complex / DNA duplex unwinding / protein localization to chromatin / DNA helicase activity / double-strand break repair via homologous recombination / single-stranded DNA binding / chromosome / DNA helicase / DNA damage response / chromatin binding / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPases associated with a variety of cellular activities ...MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLi, J. / Liu, L. / Liu, Y.
CitationJournal: Structure / Year: 2021
Title: Structural study of the N-terminal domain of human MCM8/9 complex.
Authors: Jun Li / Daqi Yu / Lan Liu / Huanhuan Liang / Qi Ouyang / Yingfang Liu /
Abstract: MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism ...MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism underlying these effects is largely unknown. Here, we report crystal structures of the N-terminal domains (NTDs) of MCM8 and MCM9, and build a ring-shaped NTD structure based on a 6.6 Å resolution cryoelectron microscopy map. This shows that the MCM8/9 complex forms a 3:3 heterohexamer in an alternating pattern. A positively charged DNA binding channel and a putative ssDNA exit pathway for fork DNA unwinding are revealed. Based on the atomic model, the potential effects of the clinical POI mutants are interpreted. Surprisingly, the zinc-finger motifs are found to be capable of binding an iron atom as well. Overall, our results provide a model for the formation of the MCM8/9 complex and provide a path for further studies.
History
DepositionDec 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Oct 27, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA helicase MCM9
B: DNA helicase MCM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3015
Polymers66,1472
Non-polymers1543
Water3,909217
1
A: DNA helicase MCM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1623
Polymers33,0741
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area15710 Å2
MethodPISA
2
B: DNA helicase MCM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1392
Polymers33,0741
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.286, 85.900, 111.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA helicase MCM9 / hMCM9 / Mini-chromosome maintenance deficient domain-containing protein 1 / Minichromosome maintenance 9


Mass: 33073.582 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: R168P,C257A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM9, C6orf61, MCMDC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NXL9, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Li2SO4, 0.1M ADA pH 6.2-6.5, 13-16% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 25165 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 38.08 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.075 / Rrim(I) all: 0.183 / Rsym value: 0.166 / Χ2: 0.884 / Net I/σ(I): 9.62
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.22 / Num. unique obs: 1250 / CC1/2: 0.806 / CC star: 0.945 / Rpim(I) all: 0.382 / Rrim(I) all: 0.821 / Rsym value: 0.723 / Χ2: 0.712 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_3139refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rossetta predicted model

Resolution: 2.55→34.11 Å / SU ML: 0.3299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0471 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1997 8.06 %
Rwork0.2083 22792 -
obs0.2128 24789 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.63 Å2
Refinement stepCycle: LAST / Resolution: 2.55→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 3 221 4570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264437
X-RAY DIFFRACTIONf_angle_d0.49796006
X-RAY DIFFRACTIONf_chiral_restr0.0437690
X-RAY DIFFRACTIONf_plane_restr0.0036772
X-RAY DIFFRACTIONf_dihedral_angle_d18.68651678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.33321340.2561525X-RAY DIFFRACTION94.31
2.61-2.680.31321420.24691609X-RAY DIFFRACTION98.26
2.68-2.760.3081380.24261593X-RAY DIFFRACTION98.58
2.76-2.850.32281410.23111596X-RAY DIFFRACTION98.92
2.85-2.950.31371420.23921627X-RAY DIFFRACTION99.44
2.95-3.070.3281430.23231622X-RAY DIFFRACTION99.6
3.07-3.210.30781430.22591628X-RAY DIFFRACTION99.33
3.21-3.380.2781420.21611631X-RAY DIFFRACTION99.55
3.38-3.590.2521440.20331641X-RAY DIFFRACTION99.5
3.59-3.870.22551420.19361624X-RAY DIFFRACTION99.38
3.87-4.260.25591460.18081662X-RAY DIFFRACTION99.34
4.26-4.870.22081450.16871648X-RAY DIFFRACTION98.35
4.87-6.140.22861450.20571665X-RAY DIFFRACTION98.69
6.14-34.110.25251500.21761721X-RAY DIFFRACTION97.14

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