[English] 日本語
Yorodumi
- PDB-9nuv: SsoPfMCM:DNA class 1c from DNA 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nuv
TitleSsoPfMCM:DNA class 1c 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 / 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: 3.51 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: Nat Commun / Year: 2026
Title: Archaeal and eukaryotic MCM rings sequentially melt DNA for replication initiation.
Authors: Sanaz Rasouli / Alexander Myasnikov / Eric J Enemark /
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 ...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.
#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
Revision 1.1Jun 17, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)456,02022
Polymers453,8228
Non-polymers2,19814
Water28816
1


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

-
Components

-
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)

-
Non-polymers , 4 types, 30 molecules

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


Mass: 427.201 Da / Num. of mol.: 4 / 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.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14925 / 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: 211.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003327431
ELECTRON MICROSCOPYf_angle_d0.55137315
ELECTRON MICROSCOPYf_chiral_restr0.04334292
ELECTRON MICROSCOPYf_plane_restr0.00334596
ELECTRON MICROSCOPYf_dihedral_angle_d14.34334208

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more