9NUS | pdb_00009nus

SsoPfMCM:DNA class 3 from DNA 1

PDB DOI: https://doi.org/10.2210/pdb9NUS/pdb
NAKB: 9NUS
EM Map EMD-49817: EMDB EMDataResource

Classification: REPLICATION, HYDROLASE/DNA
Organism(s): Saccharolobus solfataricus P2, Pyrococcus furiosus DSM 3638, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-03-19 Released: 2026-03-25
Deposition Author(s): Enemark, E.J., Rasouli, S., Myasnikov, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Archaeal and eukaryotic MCM rings sequentially melt DNA for replication initiation.

Rasouli, S., Myasnikov, A., Enemark, E.J.

(2026) Nat Commun 17

PubMed: 41916983 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-70961-8
Primary Citation Related Structures:
9NUH, 9NUI, 9NUJ, 9NUK, 9NUL, 9NUM, 9NUN, 9NUO, 9NUP, 9NUQ, 9NUR, 9NUS, 9NUT, 9NUU, 9NUV, 9NUW, 9NUX, 9NUY

PubMed Abstract:
DNA replication initiation requires local melting of fully base-paired DNA for a helicase to gain a foothold and initiate processive DNA unwinding. In eukaryotes and archaea, the helicase engine is the hexameric ring minichromosome maintenance (MCM) complex. In eukaryotes, a defined biochemical sequence assembles two Cdc45-MCM-GINS (CMG) complexes that provide limited DNA unwinding as the species that immediately precedes extensive unwinding. A prior structure revealed how MCM subunits interact with this form of DNA, but the atomic progression from undistorted DNA to this melted DNA species is unknown. Here, we present a sequential DNA melting mechanism determined by snapshots of an archaeal MCM ring with DNA in varying degrees of melting. In this mechanism, successive ATP-binding at MCM ATPase sites drives sequential discrete DNA melting steps mediated a specific MCM aromatic residue. Analysis of eukaryotic structures shows loaded MCM rings principally adopt only two molecular arrangements at the ATPase: one that does not melt DNA and one tuned to melt DNA with equivalent aromatic residues, indicating a universal sequential mechanism melts DNA in archaea and eukaryotes for replication initiation.

Organizational Affiliation

Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA.

Macromolecule Content

Total Structure Weight: 526.91 kDa
Atom Count: 34,589
Modeled Residue Count: 4,224
Deposited Residue Count: 4,411
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minichromosome maintenance protein MCM,Minichromosome maintenance protein MCM,DNA helicase	A, B, C, D, E A, B, C, D, E, F, G	613	Saccharolobus solfataricus P2, Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: MCM, SSO0774, PFDSM3638_02400 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for Q9UXG1 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q9UXG1 Go to UniProtKB: Q9UXG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UXG1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (60-MER)	H [auth X], I [auth Y]	60	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 BA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F]	BA [auth G] J [auth A] M [auth B] P [auth C] S [auth D] BA [auth G], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	AA [auth F] DA [auth G] L [auth A] O [auth B] R [auth C] AA [auth F], DA [auth G], L [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] K [auth A] N [auth B] Q [auth C] T [auth D] CA [auth G], K [auth A], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-25

Deposition Author(s):

Enemark, E.J.

Rasouli, S.

Myasnikov, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM136313
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20 GM152281
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20 GM103429