8W0E

Cryo-EM structure of a human MCM2-7 single hexamer on dsDNA

PDB DOI: https://doi.org/10.2210/pdb8W0E/pdb
EM Map EMD-43707: EMDB EMDataResource
NAKB: 8W0E

Classification: REPLICATION
Organism(s): Homo sapiens, Saccharomyces cerevisiae
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2024-02-13 Released: 2024-10-02
Deposition Author(s): Hunker, O., Yang, R., Bleichert, F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Multiple pathways for licensing human replication origins

Yang, R., Hunker, O., Wise, M., Bleichert, F.

To be published.

Macromolecule Content

Total Structure Weight: 565.1 kDa
Atom Count: 30,082
Modelled Residue Count: 3,697
Deposited Residue Count: 4,904
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 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, BM28, CCNL1, CDCL1, KIAA0030 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49736
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM3	B [auth 3]	810	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25205
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	C [auth 4]	866	Homo sapiens	Mutation(s): 1 Gene Names: MCM4, CDC21 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33991
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM5	D [auth 5]	734	Homo sapiens	Mutation(s): 0 Gene Names: MCM5, CDC46 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33992
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	E [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14566
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	F [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P33993
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	G [auth O]	25	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	H [auth S]	25	Saccharomyces cerevisiae
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 K [auth 2] MOL2 format, chain K [auth 2] mmCIF format, chain K [auth 2]	K [auth 2]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain K [auth 2] Interactions & Density Focus chain K [auth 2]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain M [auth 3] SDF format, chain Q [auth 5] SDF format, chain T [auth 6] SDF format, chain W [auth 7] MOL2 format, chain M [auth 3] MOL2 format, chain Q [auth 5] MOL2 format, chain T [auth 6] MOL2 format, chain W [auth 7] mmCIF format, chain M [auth 3] mmCIF format, chain Q [auth 5] mmCIF format, chain T [auth 6] mmCIF format, chain W [auth 7]	M [auth 3], Q [auth 5], T [auth 6], W [auth 7]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain M [auth 3] Focus chain Q [auth 5] Focus chain T [auth 6] Focus chain W [auth 7] Interactions & Density Focus chain M [auth 3] Focus chain Q [auth 5] Focus chain T [auth 6] Focus chain W [auth 7]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth 2] SDF format, chain N [auth 4] SDF format, chain O [auth 5] SDF format, chain R [auth 6] SDF format, chain U [auth 7] MOL2 format, chain I [auth 2] MOL2 format, chain N [auth 4] MOL2 format, chain O [auth 5] MOL2 format, chain R [auth 6] MOL2 format, chain U [auth 7] mmCIF format, chain I [auth 2] mmCIF format, chain N [auth 4] mmCIF format, chain O [auth 5] mmCIF format, chain R [auth 6] mmCIF format, chain U [auth 7]	I [auth 2], N [auth 4], O [auth 5], R [auth 6], U [auth 7]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth 2] Focus chain N [auth 4] Focus chain O [auth 5] Focus chain R [auth 6] Focus chain U [auth 7] Interactions & Density Focus chain I [auth 2] Focus chain N [auth 4] Focus chain O [auth 5] Focus chain R [auth 6] Focus chain U [auth 7]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth 2] SDF format, chain L [auth 3] SDF format, chain P [auth 5] SDF format, chain S [auth 6] SDF format, chain V [auth 7] MOL2 format, chain J [auth 2] MOL2 format, chain L [auth 3] MOL2 format, chain P [auth 5] MOL2 format, chain S [auth 6] MOL2 format, chain V [auth 7] mmCIF format, chain J [auth 2] mmCIF format, chain L [auth 3] mmCIF format, chain P [auth 5] mmCIF format, chain S [auth 6] mmCIF format, chain V [auth 7]	J [auth 2], L [auth 3], P [auth 5], S [auth 6], V [auth 7]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth 2] Focus chain L [auth 3] Focus chain P [auth 5] Focus chain S [auth 6] Focus chain V [auth 7] Interactions & Density Focus chain J [auth 2] Focus chain L [auth 3] Focus chain P [auth 5] Focus chain S [auth 6] Focus chain V [auth 7]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Hunker, O.

Yang, R.

Bleichert, F.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM141313
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008283
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1F31-CA278331-01