8W0G

Cryo-EM structure of a human MCM2-7 dimer

PDB DOI: https://doi.org/10.2210/pdb8W0G/pdb
EM Map EMD-43709: EMDB EMDataResource

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

Deposited: 2024-02-13 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: 3.80 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: 1,099.99 kDa
Atom Count: 56,920
Modelled Residue Count: 7,134
Deposited Residue Count: 9,708
Unique protein chains: 6

Macromolecules

Find similar proteins by:

(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

Find similar proteins by:

(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]	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

Find similar proteins by:

(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]	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

Find similar proteins by:

(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]	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	F [auth 7], L [auth F]	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

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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):

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

Revision History (Full details and data files)

Version 1.0: 2024-10-02
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

8W0G

Cryo-EM structure of a human MCM2-7 dimer

Multiple pathways for licensing human replication origins

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)