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- PDB-9nux: SsoPfMCM:DNA class 2b from DNA 2 -

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Basic information

Entry
Database: PDB / ID: 9nux
TitleSsoPfMCM:DNA class 2b from DNA 2
Components
  • DNA (60-MER)
  • Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
KeywordsREPLICATION / DNA replication / helicase / MCM
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / DNA helicase / Minichromosome maintenance protein MCM
Similarity search - Component
Biological speciesSaccharolobus solfataricus P2 (archaea)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.45 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)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
Citation
Journal: To Be Published
Title: SsoPfMCM:DNA class 2b from DNA 2
Authors: Enemark, E.J. / Rasouli, S. / Myasnikov, A.
#1: Journal: 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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 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, Cell division control protein 21,DNA helicase
B: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
C: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
D: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
E: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
F: Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase
X: DNA (60-MER)
Y: DNA (60-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,21126
Polymers453,8228
Non-polymers3,39018
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein / DNA chain , 2 types, 8 molecules ABCDEFXY

#1: Protein
Minichromosome maintenance protein MCM, Cell division control protein 21,DNA helicase


Mass: 69472.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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)
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Gene: MCM, SSO0774, PF0482 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UXG1, UniProt: Q8U3I4, DNA helicase
#2: DNA chain DNA (60-MER)


Mass: 18493.824 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: RECOMBINANT
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: 78.22 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: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 275045 / 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: 59.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004529826
ELECTRON MICROSCOPYf_angle_d0.61540454
ELECTRON MICROSCOPYf_chiral_restr0.04734665
ELECTRON MICROSCOPYf_plane_restr0.00495074
ELECTRON MICROSCOPYf_dihedral_angle_d11.11444341

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