[English] 日本語
Yorodumi
- PDB-6c5r: Crystal structure of the soluble domain of the mitochondrial calc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c5r
TitleCrystal structure of the soluble domain of the mitochondrial calcium uniporter
Componentscalcium uniporter
KeywordsCYTOSOLIC PROTEIN
Function / homology
Function and homology information


uniporter activity / uniplex complex / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / calcium channel activity / protein homotetramerization / mitochondrial inner membrane / metal ion binding / identical protein binding
Similarity search - Function
Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
Calcium uniporter protein, mitochondrial
Similarity search - Component
Biological speciesMetarhizium acridum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.09608311048 Å
AuthorsFan, C. / Fan, M. / Fastman, N. / Zhang, J. / Feng, L.
CitationJournal: Nature / Year: 2018
Title: X-ray and cryo-EM structures of the mitochondrial calcium uniporter.
Authors: Chao Fan / Minrui Fan / Benjamin J Orlando / Nathan M Fastman / Jinru Zhang / Yan Xu / Melissa G Chambers / Xiaofang Xu / Kay Perry / Maofu Liao / Liang Feng /
Abstract: Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the ...Mitochondrial calcium uptake is critical for regulating ATP production, intracellular calcium signalling, and cell death. This uptake is mediated by a highly selective calcium channel called the mitochondrial calcium uniporter (MCU). Here, we determined the structures of the pore-forming MCU proteins from two fungi by X-ray crystallography and single-particle cryo-electron microscopy. The stoichiometry, overall architecture, and individual subunit structure differed markedly from those described in the recent nuclear magnetic resonance structure of Caenorhabditis elegans MCU. We observed a dimer-of-dimer architecture across species and chemical environments, which was corroborated by biochemical experiments. Structural analyses and functional characterization uncovered the roles of key residues in the pore. These results reveal a new ion channel architecture, provide insights into calcium coordination, selectivity and conduction, and establish a structural framework for understanding the mechanism of mitochondrial calcium uniporter function.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: calcium uniporter
B: calcium uniporter
D: calcium uniporter
F: calcium uniporter
H: calcium uniporter
C: calcium uniporter
E: calcium uniporter
G: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)194,1418
Polymers194,1418
Non-polymers00
Water00
1
A: calcium uniporter
B: calcium uniporter
H: calcium uniporter
G: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)97,0714
Polymers97,0714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-80 kcal/mol
Surface area34970 Å2
MethodPISA
2
D: calcium uniporter
F: calcium uniporter
C: calcium uniporter
E: calcium uniporter


Theoretical massNumber of molelcules
Total (without water)97,0714
Polymers97,0714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-76 kcal/mol
Surface area36600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.785, 119.921, 88.005
Angle α, β, γ (deg.)90.000, 106.887, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein
calcium uniporter


Mass: 24267.676 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metarhizium acridum (strain CQMa 102) (fungus)
Strain: CQMa 102 / Gene: MAC_01752 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: E9DVV4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M glycine, pH 9.3, 15.5% PEG 4000, and 0.6 M NaNO3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09608311048→50 Å / Num. obs: 47337 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 97.3071351599 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.1
Reflection shellResolution: 3.1→3.17 Å / Num. unique obs: 3153

-
Processing

Software
NameVersionClassification
phenix.refine1.11.1_2575refinement
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 3.09608311048→42.105090976 Å / SU ML: 0.448428869909 / Cross valid method: FREE R-VALUE / σ(F): 1.33787117744 / Phase error: 34.267652959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.306400346901 2006 4.24155283968 %
Rwork0.261899995368 45288 -
obs0.263784373481 47294 99.4553445629 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.0706387757 Å2
Refinement stepCycle: LAST / Resolution: 3.09608311048→42.105090976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9966 0 0 0 9966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033520155158510173
X-RAY DIFFRACTIONf_angle_d0.66007774019413759
X-RAY DIFFRACTIONf_chiral_restr0.04289025374541534
X-RAY DIFFRACTIONf_plane_restr0.005115498047411751
X-RAY DIFFRACTIONf_dihedral_angle_d7.635566565716180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0961-3.17350.3953846292591430.3818206508493032X-RAY DIFFRACTION93.8238770686
3.1735-3.25930.3499480953911390.3713265727013253X-RAY DIFFRACTION99.8822143698
3.2593-3.35510.4032021108081460.3620978899143239X-RAY DIFFRACTION99.9409506938
3.3551-3.46340.366416433031300.3280184269293208X-RAY DIFFRACTION99.9700509134
3.4634-3.58710.3452816646521560.3086010586823227X-RAY DIFFRACTION99.9704491726
3.5871-3.73060.3212794686751410.3063175789483237X-RAY DIFFRACTION99.9408284024
3.7306-3.90030.3258588170111400.2920212236083254X-RAY DIFFRACTION99.8822836963
3.9003-4.10580.3319214628111480.2724020895573249X-RAY DIFFRACTION100
4.1058-4.36280.2772355728911440.2379419643643249X-RAY DIFFRACTION99.9705362404
4.3628-4.69920.3283572945581440.2333675766013221X-RAY DIFFRACTION100
4.6992-5.17130.2953898640891440.2295983914183279X-RAY DIFFRACTION99.9416058394
5.1713-5.91790.2944844893511410.2373268443493261X-RAY DIFFRACTION99.8532433226
5.9179-7.44920.3020323368081460.2568805939313262X-RAY DIFFRACTION99.7950219619
7.4492-42.1090.2579193646691440.2335058670913317X-RAY DIFFRACTION99.4540229885

+
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