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- PDB-9vlw: Structure of human MCM2-7 single hexamer without MCM3 CTE, state 2 -

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Basic information

Entry
Database: PDB / ID: 9vlw
TitleStructure of human MCM2-7 single hexamer without MCM3 CTE, state 2
Components(DNA replication licensing factor ...) x 6
KeywordsREPLICATION / Helicase
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / regulation of phosphorylation / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / mitotic DNA replication / CMG complex / double-strand break repair via break-induced replication / MCM complex ...Switching of origins to a post-replicative state / Unwinding of DNA / regulation of phosphorylation / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / mitotic DNA replication / CMG complex / double-strand break repair via break-induced replication / MCM complex / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA replication origin binding / cochlea development / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / cellular response to interleukin-4 / cellular response to epidermal growth factor stimulus / DNA helicase activity / Assembly of the pre-replicative complex / cellular response to xenobiotic stimulus / Orc1 removal from chromatin / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / chromosome, telomeric region / DNA replication / cell population proliferation / cilium / apoptotic process / DNA damage response / chromatin / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : ...: / DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal 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 C-terminal AAA(+) ATPase domain (MCM-CTD) 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / DNA replication licensing factor MCM6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsLam, W.H. / Fan, X. / Zhai, Y.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: To Be Published
Title: Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD
Authors: Lam, W.H. / Fan, X. / Zhai, Y.
History
DepositionJun 26, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
6: DNA replication licensing factor MCM6
4: DNA replication licensing factor MCM4
7: DNA replication licensing factor MCM7
3: DNA replication licensing factor MCM3
5: DNA replication licensing factor MCM5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,43917
Polymers530,7536
Non-polymers2,68611
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA replication licensing factor ... , 6 types, 6 molecules 264735

#1: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 102034.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2 / Production host: Homo sapiens (human) / References: UniProt: P49736
#2: Protein DNA replication licensing factor MCM6 / p105MCM


Mass: 93010.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Production host: Homo sapiens (human) / References: UniProt: Q14566, DNA helicase
#3: Protein DNA replication licensing factor MCM4 / CDC21 homolog / P1-CDC21


Mass: 96684.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM4 / Production host: Homo sapiens (human) / References: UniProt: P33991, DNA helicase
#4: Protein DNA replication licensing factor MCM7 / CDC47 homolog / P1.1-MCM3


Mass: 81411.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM7, CDC47, MCM2 / Production host: Homo sapiens (human) / References: UniProt: P33993, DNA helicase
#5: Protein DNA replication licensing factor MCM3 / DNA polymerase alpha holoenzyme-associated protein P1 / P1-MCM3 / RLF subunit beta / p102


Mass: 75205.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3 / Production host: Homo sapiens (human) / References: UniProt: P25205, DNA helicase
#6: Protein DNA replication licensing factor MCM5 / CDC46 homolog / P1-CDC46


Mass: 82406.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM5 / Production host: Homo sapiens (human) / References: UniProt: P33992, DNA helicase

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Non-polymers , 4 types, 11 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human Mini-chromosome maintenance complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.57 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES-KOH1
2250 mMPotassium chlorideKCl1
310 mMMagnesium acetateMG(OAc)21
43 mMadenosine triphosphateATP1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 47170 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 2485

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.1.2particle selection
2cryoSPARCv4.1.2initial Euler assignment
3cryoSPARCv4.1.2final Euler assignment
4cryoSPARCv4.1.2classification
5cryoSPARCv4.1.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 949477
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110899 / Symmetry type: POINT
Atomic model buildingB value: 112.6 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 7W1Y

7w1y


Accession code: 7W1Y / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.06 Å

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