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- EMDB-49806: SsoPfMCM:DNA class 1a from merged particles -

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Basic information

Entry
Database: EMDB / ID: EMD-49806
TitleSsoPfMCM:DNA class 1a from merged particles
Map dataUnsharpened map
Sample
  • Complex: Complex of MCM hexamer with DNA and Mg/ATP-gammaS
    • Protein or peptide: Minichromosome maintenance protein MCM,DNA helicase
    • DNA: DNA (60-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsDNA replication / helicase / MCM / REPLICATION / HYDROLASE- DNA complex / HYDROLASE-DNA complex
Biological speciesSaccharolobus solfataricus P2 (archaea) / Pyrococcus furiosus DSM 3638 (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsEnemark EJ / Rasouli S / Myasnikov A
Funding support United States, 3 items
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 1a from merged particles
Authors: Enemark EJ / Rasouli S / Myasnikov A
History
DepositionMar 19, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49806.png

Downloads & links

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Map

FileDownload / File: emd_49806.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.456
Minimum - Maximum-0.50841683 - 1.7836248
Average (Standard dev.)0.0011304042 (±0.089011215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_49806_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A

Fileemd_49806_half_map_1.map
Annotationhalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B

Fileemd_49806_half_map_2.map
Annotationhalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of MCM hexamer with DNA and Mg/ATP-gammaS

EntireName: Complex of MCM hexamer with DNA and Mg/ATP-gammaS
Components
  • Complex: Complex of MCM hexamer with DNA and Mg/ATP-gammaS
    • Protein or peptide: Minichromosome maintenance protein MCM,DNA helicase
    • DNA: DNA (60-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Complex of MCM hexamer with DNA and Mg/ATP-gammaS

SupramoleculeName: Complex of MCM hexamer with DNA and Mg/ATP-gammaS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: MCM is a Chimeric fusion of Saccharolobus solfataricus MCM N-terminal domain with Pyrococcus furious MCM ATPase domain
Source (natural)Organism: Saccharolobus solfataricus P2 (archaea)

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Macromolecule #1: Minichromosome maintenance protein MCM,DNA helicase

MacromoleculeName: Minichromosome maintenance protein MCM,DNA helicase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 69.472336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLEIPSKQID YRDVFIEFLT TFKGNNNQNK YIERINELVA YRKKSLIIEF SDVLSFNENL AYEIINNTKI ILPILEGALY DHILQLDPT YQRDIEKVHV RIVGIPRVIE LRKIRSTDIG KLITIDGILV KVTPVKERIY KATYKHIHPD CMQEFEWPED E EMPEVLEM ...String:
SLEIPSKQID YRDVFIEFLT TFKGNNNQNK YIERINELVA YRKKSLIIEF SDVLSFNENL AYEIINNTKI ILPILEGALY DHILQLDPT YQRDIEKVHV RIVGIPRVIE LRKIRSTDIG KLITIDGILV KVTPVKERIY KATYKHIHPD CMQEFEWPED E EMPEVLEM PTICPKCGKP GQFRLIPEKT KLIDWQKAVI QERPEEVPSG QLPRQLEIIL EDDLVDSARP GDRVKVTGIL DI KQDSPVK RGSRAVFDIY MKVSSIEVSQ KVLQELEISP EEEQIIKELA KRKDIVDAIV DSIAPAIYGY KEVKKGIALA LFG GVSRKL PDGTRLRGDI HVLLVGDPGV AKSQILRYVA NLAPRAIYTS GKSSSAAGLT AAAVRDEFTG GWVLEAGALV LADG GYALI DELDKMSDRD RSVIHEALEQ QTISISKAGI TATLNARTTV IAAANPKQGR FNRMKNPFEQ IDLPPTLLSR FDLIF VLID EPDDKIDSEV ARHILRVRRG ESEVVAPKIP HEILRKYIAY ARKNIHPVIS EEAMEEIEKY YVRMRKSVKK TKGEEE GIP PIPITARQLE ALIRLSEAHA RMRLSPIVTR EDAREAIKLM EYTLKQIAMD

UniProtKB: Minichromosome maintenance protein MCM, DNA helicase, DNA helicase

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Macromolecule #2: DNA (60-MER)

MacromoleculeName: DNA (60-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.491848 KDa
SequenceString: (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG) (DT) (DC)(DA)(DG)(DT)(DC)(DA) ...String:
(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC) (DT)(DG)(DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DT)(DG)(DA)(DC)(DT)(DG)(DA) (DC)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA)(DG) (DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT) (DC)(DA)(DG)(DT)(DC)(DA)(DG)(DT)(DC)(DA) (DG)(DT)

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 77.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4r7y

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101708
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4r7y


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9nuh:
SsoPfMCM:DNA class 1a from merged particles

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