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- PDB-9nul: SsoPfMCM:DNA class 2b from merged particles -

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Basic information

Entry
Database: PDB / ID: 9nul
TitleSsoPfMCM:DNA class 2b from merged particles
Components
  • DNA (60-MER)
  • Minichromosome maintenance protein MCM,DNA helicase
KeywordsREPLICATION / HYDROLASE/DNA / DNA replication / helicase / MCM / HYDROLASE-DNA complex
Function / homology
Function and homology information


intein-mediated protein splicing / MCM complex / single-stranded DNA helicase activity / DNA 3'-5' helicase / DNA helicase activity / single-stranded DNA binding / endonuclease activity / DNA helicase / DNA replication / cell division ...intein-mediated protein splicing / MCM complex / single-stranded DNA helicase activity / DNA 3'-5' helicase / DNA helicase activity / single-stranded DNA binding / endonuclease activity / DNA helicase / DNA replication / cell division / hydrolase activity / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
MCM protein C-terminal winged helix-turn-helix domain / : / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...MCM protein C-terminal winged helix-turn-helix domain / : / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family C-terminal AAA(+) ATPase domain (MCM-CTD) profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA helicase / Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSaccharolobus solfataricus P2 (archaea)
Pyrococcus furiosus DSM 3638 (archaea)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsEnemark, E.J. / Rasouli, S. / Myasnikov, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136313 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM152281 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103429 United States
CitationJournal: To Be Published
Title: SsoPfMCM:DNA class 2b from merged particles
Authors: Enemark, E.J. / Rasouli, S. / Myasnikov, A.
History
DepositionMar 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minichromosome maintenance protein MCM,DNA helicase
B: Minichromosome maintenance protein MCM,DNA helicase
C: Minichromosome maintenance protein MCM,DNA helicase
D: Minichromosome maintenance protein MCM,DNA helicase
E: Minichromosome maintenance protein MCM,DNA helicase
F: Minichromosome maintenance protein MCM,DNA helicase
X: DNA (60-MER)
Y: DNA (60-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,20726
Polymers453,8188
Non-polymers3,39018
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein / DNA chain , 2 types, 8 molecules ABCDEFXY

#1: Protein
Minichromosome maintenance protein MCM,DNA helicase


Mass: 69472.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea), (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea)
Gene: MCM, SSO0774, PFDSM3638_02400 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UXG1, UniProt: A0A5C0XP52, DNA helicase
#2: DNA chain DNA (60-MER)


Mass: 18491.848 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 39 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of MCM hexamer with DNA and Mg/ATP-gammaS / Type: COMPLEX
Details: MCM is a Chimeric fusion of Saccharolobus solfataricus MCM N-terminal domain with Pyrococcus furious MCM ATPase domain
Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 77 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471221 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4R7Y

4r7y


Accession code: 4R7Y / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 145.43 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002130013
ELECTRON MICROSCOPYf_angle_d0.509340743
ELECTRON MICROSCOPYf_chiral_restr0.04444697
ELECTRON MICROSCOPYf_plane_restr0.0035082
ELECTRON MICROSCOPYf_dihedral_angle_d11.22194426

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