[English] 日本語
Yorodumi
- EMDB-38109: MCM in the Apo state. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38109
TitleMCM in the Apo state.
Map dataSample of MCM_apo
Sample
  • Complex: MCM homohexamer
    • Protein or peptide: mini-chromosome maintenance complex 3
KeywordsHelicase / Replication / 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: Nat Commun / Year: 2024
Title: Open architecture of archaea MCM and dsDNA complexes resolved using monodispersed streptavidin affinity CryoEM.
Authors: Jianbing Ma / Gangshun Yi / Mingda Ye / Craig MacGregor-Chatwin / Yuewen Sheng / Ying Lu / Ming Li / Qingrong Li / Dong Wang / Robert J C Gilbert / Peijun Zhang /
Abstract: The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging ...The cryo-electron microscopy (cryoEM) method has enabled high-resolution structure determination of numerous biomolecules and complexes. Nevertheless, cryoEM sample preparation of challenging proteins and complexes, especially those with low abundance or with preferential orientation, remains a major hurdle. We developed an affinity-grid method employing monodispersed single particle streptavidin on a lipid monolayer to enhance particle absorption on the grid surface and alleviate sample exposure to the air-water interface. Using this approach, we successfully enriched the Thermococcus kodakarensis mini-chromosome maintenance complex 3 (MCM3) on cryoEM grids through biotinylation and resolved its structure. We further utilized this affinity method to tether the biotin-tagged dsDNA to selectively enrich a stable MCM3-ATP-dsDNA complex for cryoEM structure determination. Intriguingly, both MCM3 apo and dsDNA bound structures exhibit left-handed open spiral conformations, distinct from other reported MCM structures. The large open gate is sufficient to accommodate a dsDNA which could potentially be melted. The value of mspSA affinity method was further demonstrated by mitigating the issue of preferential angular distribution of HIV-1 capsid protein hexamer and RNA polymerase II elongation complex from Saccharomyces cerevisiae.
History
DepositionNov 25, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38109.png

Downloads & links

-
Map

FileDownload / File: emd_38109.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSample of MCM_apo
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 411.648 Å		1.07 Å/pix.
x 384 pix.
= 411.648 Å		1.07 Å/pix.
x 384 pix.
= 411.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.1200522 - 1.7625575
Average (Standard dev.)0.0017246403 (±0.020496562)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : MCM homohexamer

EntireName: MCM homohexamer
Components
  • Complex: MCM homohexamer
    • Protein or peptide: mini-chromosome maintenance complex 3

-
Supramolecule #1: MCM homohexamer

SupramoleculeName: MCM homohexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermococcus kodakarensis (archaea)

-
Macromolecule #1: mini-chromosome maintenance complex 3

MacromoleculeName: mini-chromosome maintenance complex 3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 76.631242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDREEMIARF AKFLREYVDD EGNEVYINRL KDLLTVTPKR SLAIDWAHLN SFDPELADEL LNNPEEAIAS AEDAIQIVLR EPPLLVERE FKVHARFYNL PKTLLVKELG SEHINKLIQV EGIITRVSEV KPFVEKAVFV CRDCGNEMVR LQRPYENLVK P AKCDACGS ...String:
MDREEMIARF AKFLREYVDD EGNEVYINRL KDLLTVTPKR SLAIDWAHLN SFDPELADEL LNNPEEAIAS AEDAIQIVLR EPPLLVERE FKVHARFYNL PKTLLVKELG SEHINKLIQV EGIITRVSEV KPFVEKAVFV CRDCGNEMVR LQRPYENLVK P AKCDACGS RNIELDVDKS RFLNFQSFRL QDRPESLKGG QMPRFVDAIL LDDLVDAALP GDRVLVTGVL RVILEQREKR PI FKKILEV NHIEQLSKEI EELEISPEDE QKIRELAKRK DIVDAIVDSI APAIWGHRIV KKGIALALFG GVQRTLPDGT KLR GESHVL LVGDPGVAKS QLLRYVANLA PRAIYTSGKS SSAAGLTAAA VRDEFTGSWV LEAGVLVLAD GGFALIDEFD KMSD RDRSA IHEALEQQTI SISKAGITAT LNSRTTVIAA ANPKFGRFNR HKSLPEQLDL PPTLLSRFDL IFLLLDEPDE KVDAS IAEH ILKVRRGEAE AVTPKIPYDL LKKYIAYARK NVHPVLSREA MEEIKRYYVK MRKGLRRGDE DGVQPIPITA RQLEAL IRL SEAHARMRLS ETVTREDARA AIEIIEAMMK TIAVDEEGNL DVSILEVGKS SKKINKIEKL VDIIKSLESE GEFGAPE EK VIEAAKQAGI GTKADIEKLL NELKSDGRVY EPRAGFYRVI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: OTHER
Details: Generated using ab-initio reconstruction routine in 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

+
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