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- PDB-8x7u: MCM in complex with dsDNA in presence of ATP. -

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Basic information

Entry
Database: PDB / ID: 8x7u
TitleMCM in complex with dsDNA in presence of ATP.
Componentsmini-chromosome maintenance complex 3
KeywordsHYDROLASE / Helicase / Replication
Function / homologyADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsMa, J. / Yi, G. / Ye, M. / MacGregor-Chatwin, C. / Sheng, Y. / Lu, Y. / Li, M. / Gilbert, R.J.C. / Zhang, P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: MCM in complex with dsDNA in presence of ATP
Authors: Ma, J. / Yi, G. / Ye, M. / MacGregor-Chatwin, C. / Sheng, Y. / Lu, Y. / Li, M. / Gilbert, R.J.C. / Zhang, P.
History
DepositionNov 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: mini-chromosome maintenance complex 3
C: mini-chromosome maintenance complex 3
B: mini-chromosome maintenance complex 3
E: mini-chromosome maintenance complex 3
A: mini-chromosome maintenance complex 3
F: mini-chromosome maintenance complex 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,39614
Polymers459,7876
Non-polymers2,6098
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
mini-chromosome maintenance complex 3


Mass: 76631.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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: MCM homohexamer in complex with dsDNA in presence of ATP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126808 / Symmetry type: POINT

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