[English] 日本語
Yorodumi
- EMDB-49806: SsoPfMCM:DNA class 1a from merged particles -

+
Open data


ID or keywords:

Loading...

-
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
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
DNA helicase / Minichromosome maintenance protein MCM
Similarity search - Component
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: 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.
History
DepositionMar 19, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49806.png

Downloads & links

-
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 °

-
Supplemental data

-
Additional map: Sharpened map

Fileemd_49806_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
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

-
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)

-
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

-
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)

-
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

-
Macromolecule #4: MAGNESIUM ION

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

-
Macromolecule #5: ZINC ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
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

+
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)

-
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

+
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