9X4K | pdb_00009x4k

A Local Refined Structure for Sld7 in Complex with Dbf4-bound Mcm6

• PDB DOI: https://doi.org/10.2210/pdb9X4K/pdb
• EM Map EMD-66551: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2025-10-11 Released: 2026-10-14 
• Deposition Author(s): Yu, D., Huo, Y., Dang, S., Zhai, Y.
• Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: integrative

Literature

A Local Refined Structure for Sld7 in Complex with Dbf4-bound Mcm6

Yu, D., Huo, Y., Dang, S., Zhai, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 253.13 kDa 
• Atom Count: 6,735 
• Modeled Residue Count: 840 
• Deposited Residue Count: 2,235 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA replication licensing factor MCM6	A [auth 6]	1,017	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53091  Go to UniProtKB:  P53091

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DDK kinase regulatory subunit DBF4	B [auth I]	704	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32325 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32325  Go to UniProtKB:  P32325

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial morphogenesis protein SLD7	C [auth M], D [auth N]	257	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q08457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08457  Go to UniProtKB:  Q08457

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.2
MODEL REFINEMENT	PHENIX	2.0-5936

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Yu, D., Huo, Y., Dang, S., Zhai, Y.

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Funding Organization	Location	Grant Number
The University Grants Committee, Research Grants Council (RGC)	Hong Kong	0000-0002-3830-0696

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release