[English] 日本語
Yorodumi
- EMDB-41588: Cryo-EM structure of human MRS2 with EDTA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41588
TitleCryo-EM structure of human MRS2 with EDTA
Map data
Sample
  • Complex: hMRS2-BRIL with EDTA
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
Keywordsmitochondria / pentamer / cation channel / METAL TRANSPORT
Function / homology
Function and homology information


mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / electron transport chain / transmembrane transport / mitochondrial inner membrane / periplasmic space / electron transfer activity / iron ion binding ...mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / electron transport chain / transmembrane transport / mitochondrial inner membrane / periplasmic space / electron transfer activity / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Magnesium transporter MRS2-like / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Magnesium transporter MRS2 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsHe Z / Mount JW / Zhang J / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS109307 United States
CitationJournal: To Be Published
Title: Human mitochondrial MRS2 is a Ca2+-regulated nonselective cation channel
Authors: He Z / Tu Y / Tsai C / Mount JW / Zhang J / Tsai M / Yuan P
History
DepositionAug 10, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_41588.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.2608466 - 6.346648
Average (Standard dev.)0.0017730417 (±0.14219312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : hMRS2-BRIL with EDTA

EntireName: hMRS2-BRIL with EDTA
Components
  • Complex: hMRS2-BRIL with EDTA
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein

-
Supramolecule #1: hMRS2-BRIL with EDTA

SupramoleculeName: hMRS2-BRIL with EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytoch...

MacromoleculeName: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
type: protein_or_peptide / ID: 1 / Details: hMRS2-dNdC-BRIL,hMRS2-dNdC-BRIL / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.471691 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR ...String:
MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR SKLHILLQNG KSLSELETDI KIFKESILEI LDEEELLEEL CVSKWSDPQV FEKSSAGIDH AEEMELLLEN YY RLADDLS NAARELRVLI DDSQSIIFIN LDSHRNVMMR LNLQLTMGTF SLSLFGLMGV AFGMNLESSL EEDHRIFWLI TGI MFMGSG LIWRRLLSFL GRQLEAPLPP MMASLPKKTL LADRSMELKN SLRLDADLED NWETLNDNLK VIEKADNAAQ VKDA LTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLSNS LEVL FQ

UniProtKB: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClsodium chloride
0.04 mMGDNglyco-diosgenin
10.0 mMEDTAEthylenediaminetetraacetic acid

Details: 20 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA and 0.04 mM GDN
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3477 / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000

+
Image processing

Particle selectionNumber selected: 1249448
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ts1

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 406358
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8ts2:
Cryo-EM structure of human MRS2 with EDTA

+
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://pdbjlc1.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