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- EMDB-19625: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-19625
TitleH. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant
Map dataH. sapiens MCM double hexamer containing the MCM5 AG mutation
Sample
  • Complex: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant
KeywordsAAA+ ATPase / DNA helicase / REPLICATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsPuehringer T / Weissmann F / Greiwe J / Diffley JFX / Costa A
Funding support United Kingdom, European Union, Germany, 5 items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2002, CC2009 United Kingdom
European Research Council (ERC)820102European Union
Boehringer Ingelheim Fonds (BIF) Germany
Wellcome Trust219527/Z/19/Z United Kingdom
European Research Council (ERC)101020432-MeChroRepEuropean Union
Citation
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.
#1: Journal: Biorxiv / Year: 2024
Title: MCM Double Hexamer Loading Visualised with Human Proteins
Authors: Weissmann F / Greiwe JF / Puhringer T / Miller TCR / Diffley JFX / Costa A
History
DepositionFeb 13, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19625.png

Downloads & links

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Map

FileDownload / File: emd_19625.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH. sapiens MCM double hexamer containing the MCM5 AG mutation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 300 pix.
= 474. Å		1.58 Å/pix.
x 300 pix.
= 474. Å		1.58 Å/pix.
x 300 pix.
= 474. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-2.6419272 - 6.018704
Average (Standard dev.)0.0031675657 (±0.2242967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 474.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2 of the main map

Fileemd_19625_half_map_1.map
AnnotationHalf map 2 of the main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the main map

Fileemd_19625_half_map_2.map
AnnotationHalf map 1 of the main map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant

EntireName: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant
Components
  • Complex: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant

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Supramolecule #1: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant

SupramoleculeName: H. sapiens MCM double hexamer containing the MCM5 R195A/L209G mutant
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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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: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified Homo sapiens ORC1-5, CDC6, CDT1 and the MCM2-7 complex containing the MCM5 R195A/L209G mutant were incubated with an origin DNA template. After 30 minutes at 37 degrees C, the reaction was diluted 40% and 4 micro litres were applied to cryo-EM grids.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 13203 / Average exposure time: 1.12 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 92000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE / Details: Ab intio model in cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.0) / Software - details: Local refinement / Number images used: 72117
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.0) / Software - details: Local refinement
FSC plot (resolution estimation)

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