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- PDB-7wi7: Crystal structure of human MCM8/9 complex -

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Basic information

Entry
Database: PDB / ID: 7wi7
TitleCrystal structure of human MCM8/9 complex
Components
  • DNA helicase MCM8
  • DNA helicase MCM9
KeywordsDNA BINDING PROTEIN / MCM8 / MCM9 / Helicase
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 / CDC6 association with the ORC:origin complex / female gamete generation / MutSalpha complex binding / 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 / CDC6 association with the ORC:origin complex / female gamete generation / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / Unwinding of DNA / MCM complex / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / protein localization to chromatin / DNA helicase activity / 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 / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / MCM8 winged helix domain / 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 ...: / MCM8 winged helix domain / 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 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA helicase MCM9 / DNA helicase MCM8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.6 Å
AuthorsLi, J. / Liu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2019ZT08Y464 China
Other governmentJCYJ20200109142412265 China
CitationJournal: To Be Published
Title: Crystal structure of human MCM8/9 complex
Authors: Li, J. / Liu, Y.
History
DepositionJan 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.2Nov 29, 2023Group: 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 MCM8
B: DNA helicase MCM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,8004
Polymers164,6702
Non-polymers1312
Water00
1
A: DNA helicase MCM8
B: DNA helicase MCM9
hetero molecules

A: DNA helicase MCM8
B: DNA helicase MCM9
hetero molecules

A: DNA helicase MCM8
B: DNA helicase MCM9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,40112
Polymers494,0096
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area20700 Å2
ΔGint-77 kcal/mol
Surface area160280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.616, 185.616, 185.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA helicase MCM8 / Minichromosome maintenance 8


Mass: 87820.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM8, C20orf154 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJA3, DNA helicase
#2: Protein DNA helicase MCM9 / hMCM9 / Mini-chromosome maintenance deficient domain-containing protein 1 / Minichromosome maintenance 9


Mass: 76848.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM9, C6orf61, MCMDC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NXL9, DNA helicase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propone, pH 6.0-7.5, 0.6M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 6.6→41.5 Å / Num. obs: 4153 / % possible obs: 97.81 % / Redundancy: 13.7 % / Biso Wilson estimate: 431.51 Å2 / CC1/2: 0.99 / Rsym value: 0.061 / Net I/σ(I): 39.8
Reflection shellResolution: 6.6→6.71 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 418 / Rsym value: 0.768 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot0.8.2model building
PHENIX1.17_3644refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DP3, 7DPD

7dp3

7dpd


Resolution: 6.6→41.5 Å / SU ML: 1.8622 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.0802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3977 415 10.11 %
Rwork0.3209 3689 -
obs0.3287 4104 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 627.19 Å2
Refinement stepCycle: LAST / Resolution: 6.6→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8833 0 2 0 8835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198973
X-RAY DIFFRACTIONf_angle_d0.513512117
X-RAY DIFFRACTIONf_chiral_restr0.04051419
X-RAY DIFFRACTIONf_plane_restr0.00291540
X-RAY DIFFRACTIONf_dihedral_angle_d13.44563362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.6-7.550.5881390.43011222X-RAY DIFFRACTION99.85
7.56-9.50.41291370.36891226X-RAY DIFFRACTION99.2
9.51-41.50.36421390.28421241X-RAY DIFFRACTION96.17
Refinement TLS params.Method: refined / Origin x: 18.1444696396 Å / Origin y: 21.367660008 Å / Origin z: -19.5298083088 Å
111213212223313233
T4.99836302268 Å2-0.543401242338 Å2-0.0191114077517 Å2-4.23780287903 Å20.657088483685 Å2--4.06247101592 Å2
L2.64533531031 °20.491309327563 °21.21832735543 °2-0.649224225774 °22.45791422994 °2--1.40395027046 °2
S-0.448929466623 Å °0.867015270384 Å °0.615633413389 Å °-0.286172695234 Å °0.578134500216 Å °-0.0575913553684 Å °-0.770761806761 Å °0.402695207081 Å °-1.27508040611E-5 Å °
Refinement TLS groupSelection details: all

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