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- EMDB-49821: SsoPfMCM:DNA class 2a from DNA 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-49821
TitleSsoPfMCM:DNA class 2a from DNA 2
Map dataUnsharpened map
Sample
  • Complex: Complex of MCM hexamer with DNA and Mg/ATP-gammaS
    • Protein or peptide: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
    • DNA: DNA (60-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water
KeywordsDNA replication / helicase / MCM / REPLICATION
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 / metal ion 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
DNA helicase / Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSaccharolobus solfataricus P2 (archaea) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 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)R35GM136313 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM152281 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103429 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 19, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49821.png

Downloads & links

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Map

FileDownload / File: emd_49821.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: 0.381
Minimum - Maximum-0.6561383 - 2.2307458
Average (Standard dev.)-0.0010832374 (±0.08264976)
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_49821_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 B

Fileemd_49821_half_map_1.map
Annotationhalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A

Fileemd_49821_half_map_2.map
Annotationhalf-map A
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, Cell division control protein 21,DNA helicase
    • DNA: DNA (60-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • 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, Cell division control pro...

MacromoleculeName: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
type: protein_or_peptide / ID: 1
Details: N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus ...Details: N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966),N-term Saccharolobus solfataricus P2, ATPase Pyrococcus furiosus DSM 3638 The protein construct exactly matches that of PDB 4R7Y. This is a chimeric fusion of the Saccharolobus solfataricus MCM N-terminal domain (SsoMCM amino acids 1-269) with the Pyrococcus furious MCM ATPase domain (PfMCM amino acids 257-361/729-966). The native PfMCM has an intein (PfMCM aa 362-728) that is removed. The expression construct for this protein has genetically removed the intein. To simplify model building and refinement, all amino acids were numbered sequentially based on the the SsoMCM sequence. Could the PfMCM portion have its amino acid numbers updated to match PDB 4R7Y? Segment 1: Current: (Q270-L374). Add 987. New: (Q1257-L1361) Segment 2: Current: (T375-D612). Add 1354. New: (T1729-D1966)
Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharolobus solfataricus P2 (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: 18.493824 KDa
SequenceString: (DT)(DC)(DC)(DG)(DT)(DC)(DT)(DC)(DA)(DC) (DA)(DG)(DT)(DA)(DA)(DC)(DA)(DA)(DC)(DC) (DC)(DT)(DC)(DC)(DG)(DC)(DC)(DT)(DG) (DA)(DT)(DC)(DA)(DG)(DG)(DC)(DG)(DG)(DA) (DG) (DG)(DG)(DT)(DT)(DG)(DT) ...String:
(DT)(DC)(DC)(DG)(DT)(DC)(DT)(DC)(DA)(DC) (DA)(DG)(DT)(DA)(DA)(DC)(DA)(DA)(DC)(DC) (DC)(DT)(DC)(DC)(DG)(DC)(DC)(DT)(DG) (DA)(DT)(DC)(DA)(DG)(DG)(DC)(DG)(DG)(DA) (DG) (DG)(DG)(DT)(DT)(DG)(DT)(DT)(DA) (DC)(DT)(DG)(DT)(DG)(DA)(DG)(DA)(DC)(DG) (DG)(DA)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / 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 #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 21 / 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: 78.22 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235648
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-9nuw:
SsoPfMCM:DNA class 2a from DNA 2

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