9CAQ

Cryo-EM structure of a human MCM2-7 double hexamer formed from independently loaded MCM2-7 single hexamers

PDB DOI: https://doi.org/10.2210/pdb9CAQ/pdb
NAKB: 9CAQ
EM Map EMD-45400: EMDB EMDataResource

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

Deposited: 2024-06-17 Released: 2024-10-02
Deposition Author(s): Yang, R., Hunker, O., 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: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 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: 1,126.82 kDa
Atom Count: 60,375
Modelled Residue Count: 7,456
Deposited Residue Count: 9,798
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], G [auth A]	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], H [auth B]	808	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], I [auth C]	863	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], J [auth D]	737	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], K [auth E]	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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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	F [auth 7], L [auth F]	722	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 (44-MER)	M [auth O]	44	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (44-MER)	N [auth S]	44	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 EA [auth A] SDF format, chain Q [auth 2] MOL2 format, chain EA [auth A] MOL2 format, chain Q [auth 2] mmCIF format, chain EA [auth A] mmCIF format, chain Q [auth 2]	EA [auth A], Q [auth 2]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain EA [auth A] Focus chain Q [auth 2] Interactions & Density Focus chain EA [auth A] Focus chain Q [auth 2]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain BA [auth 7] SDF format, chain FA [auth B] SDF format, chain KA [auth D] SDF format, chain NA [auth E] SDF format, chain QA [auth F] SDF format, chain R [auth 3] SDF format, chain T [auth 4] SDF format, chain W [auth 5] MOL2 format, chain BA [auth 7] MOL2 format, chain FA [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth 3] MOL2 format, chain T [auth 4] MOL2 format, chain W [auth 5] mmCIF format, chain BA [auth 7] mmCIF format, chain FA [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain NA [auth E] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth 3] mmCIF format, chain T [auth 4] mmCIF format, chain W [auth 5]	BA [auth 7] FA [auth B] KA [auth D] NA [auth E] QA [auth F] BA [auth 7], FA [auth B], KA [auth D], NA [auth E], QA [auth F], R [auth 3], T [auth 4], W [auth 5]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth 7] Focus chain FA [auth B] Focus chain KA [auth D] Focus chain NA [auth E] Focus chain QA [auth F] Focus chain R [auth 3] Focus chain T [auth 4] Focus chain W [auth 5] Interactions & Density Focus chain BA [auth 7] Focus chain FA [auth B] Focus chain KA [auth D] Focus chain NA [auth E] Focus chain QA [auth F] Focus chain R [auth 3] Focus chain T [auth 4] Focus chain W [auth 5]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain GA [auth C] SDF format, chain IA [auth D] SDF format, chain LA [auth E] SDF format, chain O [auth 2] SDF format, chain OA [auth F] SDF format, chain S [auth 4] SDF format, chain U [auth 5] SDF format, chain X [auth 6] SDF format, chain Z [auth 7] MOL2 format, chain CA [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth 2] MOL2 format, chain OA [auth F] MOL2 format, chain S [auth 4] MOL2 format, chain U [auth 5] MOL2 format, chain X [auth 6] MOL2 format, chain Z [auth 7] mmCIF format, chain CA [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth 2] mmCIF format, chain OA [auth F] mmCIF format, chain S [auth 4] mmCIF format, chain U [auth 5] mmCIF format, chain X [auth 6] mmCIF format, chain Z [auth 7]	CA [auth A] GA [auth C] IA [auth D] LA [auth E] O [auth 2] CA [auth A], GA [auth C], IA [auth D], LA [auth E], O [auth 2], OA [auth F], S [auth 4], U [auth 5], X [auth 6], Z [auth 7]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain O [auth 2] Focus chain OA [auth F] Focus chain S [auth 4] Focus chain U [auth 5] Focus chain X [auth 6] Focus chain Z [auth 7] Interactions & Density Focus chain CA [auth A] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain O [auth 2] Focus chain OA [auth F] Focus chain S [auth 4] Focus chain U [auth 5] Focus chain X [auth 6] Focus chain Z [auth 7]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth 7] SDF format, chain DA [auth A] SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain MA [auth E] SDF format, chain P [auth 2] SDF format, chain PA [auth F] SDF format, chain V [auth 5] SDF format, chain Y [auth 6] MOL2 format, chain AA [auth 7] MOL2 format, chain DA [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain P [auth 2] MOL2 format, chain PA [auth F] MOL2 format, chain V [auth 5] MOL2 format, chain Y [auth 6] mmCIF format, chain AA [auth 7] mmCIF format, chain DA [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain P [auth 2] mmCIF format, chain PA [auth F] mmCIF format, chain V [auth 5] mmCIF format, chain Y [auth 6]	AA [auth 7] DA [auth A] HA [auth D] JA [auth D] MA [auth E] AA [auth 7], DA [auth A], HA [auth D], JA [auth D], MA [auth E], P [auth 2], PA [auth F], V [auth 5], Y [auth 6]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth 7] Focus chain DA [auth A] Focus chain HA [auth D] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain P [auth 2] Focus chain PA [auth F] Focus chain V [auth 5] Focus chain Y [auth 6] Interactions & Density Focus chain AA [auth 7] Focus chain DA [auth A] Focus chain HA [auth D] Focus chain JA [auth D] Focus chain MA [auth E] Focus chain P [auth 2] Focus chain PA [auth F] Focus chain V [auth 5] Focus chain Y [auth 6]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Yang, R.

Hunker, O.

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
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	S10OD023603