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- PDB-7dp3: Human MCM8 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7dp3
TitleHuman MCM8 N-terminal domain
ComponentsDNA helicase MCM8
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 / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / E2F-enabled inhibition of pre-replication complex formation ...MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / E2F-enabled inhibition of pre-replication complex formation / Unwinding of DNA / MCM complex / DNA duplex unwinding / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / protein localization to chromatin / helicase activity / double-strand break repair via homologous recombination / Orc1 removal from chromatin / single-stranded DNA binding / chromosome / DNA helicase / protein stabilization / DNA damage response / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB 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 / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB 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 17, 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 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA helicase MCM8
B: DNA helicase MCM8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4594
Polymers74,3282
Non-polymers1312
Water4,648258
1
A: DNA helicase MCM8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2302
Polymers37,1641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA helicase MCM8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2302
Polymers37,1641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.017, 52.028, 137.221
Angle α, β, γ (deg.)90.000, 91.864, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DNA helicase MCM8 / Minichromosome maintenance 8


Mass: 37164.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM8, C20orf154 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJA3, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M (NH4)2SO4, 20.5-22% (w/v) PEG 3350, 0.1M Tris-Cl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 21244 / % possible obs: 98.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 32.54 Å2 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.06 / Χ2: 0.89 / Net I/σ(I): 10.79
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1009 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.333 / Rsym value: 0.684 / Χ2: 0.81 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
HKL-3000data scaling
Cootmodel building
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4POF

4pof


Resolution: 2.55→48.65 Å / SU ML: 0.3691 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.4028
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2718 1883 9.99 %
Rwork0.2137 16961 -
obs0.2194 18844 87.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.27 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 2 262 4663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164505
X-RAY DIFFRACTIONf_angle_d0.55596104
X-RAY DIFFRACTIONf_chiral_restr0.0418701
X-RAY DIFFRACTIONf_plane_restr0.0039780
X-RAY DIFFRACTIONf_dihedral_angle_d13.62231704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.620.3528780.2788666X-RAY DIFFRACTION46.01
2.62-2.70.3679970.2646896X-RAY DIFFRACTION60.18
2.7-2.780.35991030.2661012X-RAY DIFFRACTION68.32
2.78-2.880.31691500.23831218X-RAY DIFFRACTION82.41
2.88-30.30941540.23181346X-RAY DIFFRACTION93.17
3-3.130.31611600.23661414X-RAY DIFFRACTION95.39
3.13-3.30.2651610.23671475X-RAY DIFFRACTION97.73
3.3-3.510.25581600.20641451X-RAY DIFFRACTION99.26
3.51-3.780.27211680.20461468X-RAY DIFFRACTION99.27
3.78-4.160.24821570.19351487X-RAY DIFFRACTION99.7
4.16-4.760.21111680.17491493X-RAY DIFFRACTION99.7
4.76-5.990.2531610.20791514X-RAY DIFFRACTION99.94
5.99-48.650.29081660.21931521X-RAY DIFFRACTION97.23

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