9VLW | pdb_00009vlw

Structure of human MCM2-7 single hexamer without MCM3 CTE, state 2

PDB DOI: https://doi.org/10.2210/pdb9VLW/pdb
EM Map EMD-65170: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-06-26 Released: 2026-05-20
Deposition Author(s): Lam, W.H., Fan, X., Zhai, Y.
Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of human MCM2-7 single hexamer with MCM3-WHD attached to MCM2-CTD

Lam, W.H., Fan, X., Zhai, Y.

To be published.

Macromolecule Content

Total Structure Weight: 533.44 kDa
Atom Count: 28,206
Modeled Residue Count: 3,686
Deposited Residue Count: 4,711
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	A [auth 2]	904	Homo sapiens	Mutation(s): 0 Gene Names: MCM2 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P49736 (Homo sapiens) Explore P49736 Go to UniProtKB: P49736
PHAROS: P49736 GTEx: ENSG00000073111
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49736
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	B [auth 6]	821	Homo sapiens	Mutation(s): 0 Gene Names: MCM6 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q14566 (Homo sapiens) Explore Q14566 Go to UniProtKB: Q14566
PHAROS: Q14566 GTEx: ENSG00000076003
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14566
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	C [auth 4]	863	Homo sapiens	Mutation(s): 0 Gene Names: MCM4 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33991 (Homo sapiens) Explore P33991 Go to UniProtKB: P33991
PHAROS: P33991 GTEx: ENSG00000104738
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33991
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	D [auth 7]	719	Homo sapiens	Mutation(s): 0 Gene Names: MCM7, CDC47, MCM2 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33993 (Homo sapiens) Explore P33993 Go to UniProtKB: P33993
PHAROS: P33993 GTEx: ENSG00000166508
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33993
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM3	E [auth 3]	670	Homo sapiens	Mutation(s): 0 Gene Names: MCM3 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P25205 (Homo sapiens) Explore P25205 Go to UniProtKB: P25205
PHAROS: P25205 GTEx: ENSG00000112118
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25205
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM5	F [auth 5]	734	Homo sapiens	Mutation(s): 0 Gene Names: MCM5 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P33992 (Homo sapiens) Explore P33992 Go to UniProtKB: P33992
PHAROS: P33992 GTEx: ENSG00000100297
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33992
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth 2] SDF format, chain J [auth 6] SDF format, chain M [auth 4] MOL2 format, chain H [auth 2] MOL2 format, chain J [auth 6] MOL2 format, chain M [auth 4] mmCIF format, chain H [auth 2] mmCIF format, chain J [auth 6] mmCIF format, chain M [auth 4]	H [auth 2], J [auth 6], M [auth 4]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth 2] Focus chain J [auth 6] Focus chain M [auth 4] Interactions & Density Focus chain H [auth 2] Focus chain J [auth 6] Focus chain M [auth 4]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain O [auth 7] SDF format, chain Q [auth 3] MOL2 format, chain O [auth 7] MOL2 format, chain Q [auth 3] mmCIF format, chain O [auth 7] mmCIF format, chain Q [auth 3]	O [auth 7], Q [auth 3]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain O [auth 7] Focus chain Q [auth 3] Interactions & Density Focus chain O [auth 7] Focus chain Q [auth 3]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth 2] SDF format, chain K [auth 6] SDF format, chain L [auth 4] SDF format, chain P [auth 7] MOL2 format, chain I [auth 2] MOL2 format, chain K [auth 6] MOL2 format, chain L [auth 4] MOL2 format, chain P [auth 7] mmCIF format, chain I [auth 2] mmCIF format, chain K [auth 6] mmCIF format, chain L [auth 4] mmCIF format, chain P [auth 7]	I [auth 2], K [auth 6], L [auth 4], P [auth 7]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth 2] Focus chain K [auth 6] Focus chain L [auth 4] Focus chain P [auth 7] Interactions & Density Focus chain I [auth 2] Focus chain K [auth 6] Focus chain L [auth 4] Focus chain P [auth 7]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth 2] SDF format, chain N [auth 4] MOL2 format, chain G [auth 2] MOL2 format, chain N [auth 4] mmCIF format, chain G [auth 2] mmCIF format, chain N [auth 4]	G [auth 2], N [auth 4]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth 2] Focus chain N [auth 4] Interactions & Density Focus chain G [auth 2] Focus chain N [auth 4]