9TH8 | pdb_00009th8

Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

PDB DOI: https://doi.org/10.2210/pdb9TH8/pdb
EM Map EMD-55918: EMDB EMDataResource

Classification: REPLICATION
Organism(s): Saccharomyces cerevisiae
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-12-03 Released: 2026-08-26
Deposition Author(s): Saleh, A., Noguchi, Y., Schneider, S., Aramayo, R., Speck, C.
Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation

Noguchi, Y., Saleh, A., Schneider, S., Ivanova, M.E., Chen, Z.A., Ranjha, L., Aramayo, R., Tognetti, S., Faull, S.V., Rappsilber, J., Speck, C.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-76309-6

Macromolecule Content

Total Structure Weight: 1,435.15 kDa
Atom Count: 72,267
Modeled Residue Count: 8,913
Deposited Residue Count: 12,513
Unique protein chains: 9
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM2	C [auth B], I [auth 2]	868	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM2, YBL023C, YBL0438 EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29469 Go to UniProtKB: P29469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29469
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 MCM3	D [auth C], J [auth 3]	971	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM3, YEL032W, SYGP-ORF23 EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24279 Go to UniProtKB: P24279
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24279
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM4	E [auth D], K [auth 4]	933	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13 EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30665 Go to UniProtKB: P30665
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30665
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Minichromosome maintenance protein 5	F [auth E], L [auth 5]	775	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM5, CDC46, YLR274W, L9328.1 EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29496 Go to UniProtKB: P29496
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29496
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	G [auth F], M [auth 6]	1,017	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM6, YGL201C EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53091 Go to UniProtKB: P53091
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53091
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM7	H [auth G], N [auth 7]	845	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MCM7, CDC47, YBR202W, YBR1441 EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38132 Go to UniProtKB: P38132
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38132
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication regulator SLD3	O [auth X]	668	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SLD3, YGL113W, G2980
UniProt
Find proteins for P53135 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53135 Go to UniProtKB: P53135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53135
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 45	P [auth Z]	650	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC45, SLD4, YLR103C, L8004.11
UniProt
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08032 Go to UniProtKB: Q08032
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08032
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial morphogenesis protein SLD7	Q [auth Y]	257	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: SLD7, YOR060C, YOR29-11
UniProt
Find proteins for Q08457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08457 Go to UniProtKB: Q08457
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q08457
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
dsDNA (60-MER)	A [auth O]	60	Saccharomyces cerevisiae
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
dsDNA (60-MER)	B [auth S]	60	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain V [auth E] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain HA [auth 7] SDF format, chain EA [auth 5] SDF format, chain CA [auth 3] SDF format, chain AA [auth 2] MOL2 format, chain Y [auth G] MOL2 format, chain V [auth E] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain HA [auth 7] MOL2 format, chain EA [auth 5] MOL2 format, chain CA [auth 3] MOL2 format, chain AA [auth 2] mmCIF format, chain Y [auth G] mmCIF format, chain V [auth E] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain HA [auth 7] mmCIF format, chain EA [auth 5] mmCIF format, chain CA [auth 3] mmCIF format, chain AA [auth 2]	AA [auth 2] CA [auth 3] EA [auth 5] HA [auth 7] R [auth B] AA [auth 2], CA [auth 3], EA [auth 5], HA [auth 7], R [auth B], T [auth C], V [auth E], Y [auth G]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain AA [auth 2] Focus chain CA [auth 3] Focus chain EA [auth 5] Focus chain HA [auth 7] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth E] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth 2] Focus chain CA [auth 3] Focus chain EA [auth 5] Focus chain HA [auth 7] Focus chain R [auth B] Focus chain T [auth C] Focus chain V [auth E] Focus chain Y [auth G]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain X [auth F] SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain S [auth B] SDF format, chain IA [auth 7] SDF format, chain GA [auth 6] SDF format, chain FA [auth 5] SDF format, chain DA [auth 4] SDF format, chain BA [auth 2] MOL2 format, chain Z [auth G] MOL2 format, chain X [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain S [auth B] MOL2 format, chain IA [auth 7] MOL2 format, chain GA [auth 6] MOL2 format, chain FA [auth 5] MOL2 format, chain DA [auth 4] MOL2 format, chain BA [auth 2] mmCIF format, chain Z [auth G] mmCIF format, chain X [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain S [auth B] mmCIF format, chain IA [auth 7] mmCIF format, chain GA [auth 6] mmCIF format, chain FA [auth 5] mmCIF format, chain DA [auth 4] mmCIF format, chain BA [auth 2]	BA [auth 2] DA [auth 4] FA [auth 5] GA [auth 6] IA [auth 7] BA [auth 2], DA [auth 4], FA [auth 5], GA [auth 6], IA [auth 7], S [auth B], U [auth D], W [auth E], X [auth F], Z [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth 2] Focus chain DA [auth 4] Focus chain FA [auth 5] Focus chain GA [auth 6] Focus chain IA [auth 7] Focus chain S [auth B] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth 2] Focus chain DA [auth 4] Focus chain FA [auth 5] Focus chain GA [auth 6] Focus chain IA [auth 7] Focus chain S [auth B] Focus chain U [auth D] Focus chain W [auth E] Focus chain X [auth F] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
RECONSTRUCTION	RELION	4.0
RECONSTRUCTION	PHENIX	1.21.2-5419
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	107903/Z/15/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T005378/1
Cancer Research UK	United Kingdom	DRCNPG-May21/100006

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9TH8 | pdb_00009th8

Cryo-EM structure of MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

Literature

Structural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation

Biological Assembly 1

Macromolecules

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 1

Sequence Annotations

Entity ID: 2

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)