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- EMDB-38110: Structure of MCM_apo before local refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-38110
TitleStructure of MCM_apo before local refinement
Map dataStructure of MCM_apo before local refinement
Sample
  • Complex: mini-chromosome maintenance complex 3
    • Protein or peptide: Thermococcus kodakarensis
KeywordsReplication / helicase / HYDROLASE
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMa J / Yi G / Ye M / MacGregor-Chatwin C / Sheng Y / Lu Y / Li M / Gilbert RJC / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Structure of MCM_apo before local refinement
Authors: Jianbing M / Gangshun Y / Mingda Y / Craig MGC / Yuewen S / Ying L / Ming L / Gilbert RJC / Peijun Z
History
DepositionNov 25, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38110.png

Downloads & links

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Map

FileDownload / File: emd_38110.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of MCM_apo before local refinement
Voxel sizeX=Y=Z: 1.072 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.3047084 - 1.6263434
Average (Standard dev.)0.0008403847 (±0.018418526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 411.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of MCM apo before local refinement

Fileemd_38110_half_map_1.map
AnnotationHalf map A of MCM_apo before local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of MCM apo before local refinement

Fileemd_38110_half_map_2.map
AnnotationHalf map B of MCM_apo before local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mini-chromosome maintenance complex 3

EntireName: mini-chromosome maintenance complex 3
Components
  • Complex: mini-chromosome maintenance complex 3
    • Protein or peptide: Thermococcus kodakarensis

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Supramolecule #1: mini-chromosome maintenance complex 3

SupramoleculeName: mini-chromosome maintenance complex 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermococcus kodakarensis (archaea)

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Macromolecule #1: Thermococcus kodakarensis

MacromoleculeName: Thermococcus kodakarensis / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: mdreemiarf akflreyvd d egnevyin rl kdlltvt pkr slaidw ahln sfdpe ladel lnnp eeaias aed aiqivlr ep pllveref k vharfynlp ktllvkelgs ehinkliqv e giitrvse vk pfvekav fvc rdcgne mvrl qrpye ...String:
mdreemiarf akflreyvd d egnevyin rl kdlltvt pkr slaidw ahln sfdpe ladel lnnp eeaias aed aiqivlr ep pllveref k vharfynlp ktllvkelgs ehinkliqv e giitrvse vk pfvekav fvc rdcgne mvrl qrpye nlvkp akcd acgsrn iel dvdksrf ln fqsfrlqd r peslkggqm prfvdailld dlvdaalpg d rvlvtgvl rv ileqrek rpi fkkile vnhi eqlsk eieel eisp edeqki rel akrkdiv da ivdsiapa i wghrivkkg ialalfggvq rtlpdgtkl r geshvllv gd pgvaksq llr yvanla prai ytsgk sssaa gl t aaavrde ft gswvleag v lvladggfa lidefdkmsd rdrsaihea l eqq ti s iskagitat lnsrttviaa anpkfgrfn r hkslpeql dl pptllsr fdl ifllld epde kvdas iaehi lkvr rgeaea vtp kipydll kk yiayarkn v hpvlsream eeikryyvkm rkglrrgde d gvqpipit ar qlealir lse aharmr lset vtred araai eiie ammkti avd eegnldv si levgkssk k inkieklvd iikslesege fgapeekvi e aakqagig tk adiekll nel ksdgrv yepr agfyr vi

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initial model by CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 445096
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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