9NUN | pdb_00009nun

SsoPfMCM:DNA class 1a from DNA 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NUN

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

  • 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: 456.92 kDa 
  • Atom Count: 29,677 
  • Modeled Residue Count: 3,604 
  • Deposited Residue Count: 3,798 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein MCM,DNA helicase
A, B, C, D, E
A, B, C, D, E, F
613Saccharolobus solfataricus P2Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: MCMSSO0774PFDSM3638_02400
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
Find proteins for A0A5C0XP52 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore A0A5C0XP52 
Go to UniProtKB:  A0A5C0XP52
Find proteins for Q9UXG1 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXG1 
Go to UniProtKB:  Q9UXG1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9UXG1A0A5C0XP52
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (60-MER)G [auth X],
H [auth Y]
60synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A]
N [auth B]
Q [auth C]
T [auth D]
W [auth E]
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
J [auth A]
M [auth B]
P [auth C]
S [auth D]
V [auth E]
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136313
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM152281
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP20 GM103429

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Data collection, Database references