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- PDB-5id3: Solution structure of the pore-forming region of C. elegans Mitoc... -

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Basic information

Entry
Database: PDB / ID: 5id3
TitleSolution structure of the pore-forming region of C. elegans Mitochondrial Calcium Uniporter (MCU)
ComponentsMitochondrial Calcium Uniporter
KeywordsTRANSPORT PROTEIN / calcium channel / mitochondria / pentamer / N-terminal domain truncation / Structural Genomics / PSI-Biology / Membrane Protein Structures by Solution NMR / MPSbyNMR
Function / homology
Function and homology information


Mitochondrial calcium ion transport / Processing of SMDT1 / : / uniporter activity / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / mitochondrial calcium ion homeostasis / regulation of wound healing / regulation of reactive oxygen species biosynthetic process ...Mitochondrial calcium ion transport / Processing of SMDT1 / : / uniporter activity / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / mitochondrial calcium ion homeostasis / regulation of wound healing / regulation of reactive oxygen species biosynthetic process / calcium channel activity / protein homooligomerization / 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 speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsOxenoid, K. / Dong, Y. / Cao, C. / Cui, T. / Sancak, Y. / Markhard, A.L. / Grabarek, Z. / Kong, L. / Liu, Z. / Ouyang, B. ...Oxenoid, K. / Dong, Y. / Cao, C. / Cui, T. / Sancak, Y. / Markhard, A.L. / Grabarek, Z. / Kong, L. / Liu, Z. / Ouyang, B. / Cong, Y. / Mootha, V.K. / Chou, J.J. / Membrane Protein Structures by Solution NMR (MPSbyNMR)
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094608 United States
CASXDB08030301 China
CitationJournal: Nature / Year: 2016
Title: Architecture of the mitochondrial calcium uniporter.
Authors: Oxenoid, K. / Dong, Y. / Cao, C. / Cui, T. / Sancak, Y. / Markhard, A.L. / Grabarek, Z. / Kong, L. / Liu, Z. / Ouyang, B. / Cong, Y. / Mootha, V.K. / Chou, J.J.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitochondrial Calcium Uniporter
B: Mitochondrial Calcium Uniporter
C: Mitochondrial Calcium Uniporter
D: Mitochondrial Calcium Uniporter
E: Mitochondrial Calcium Uniporter


Theoretical massNumber of molelcules
Total (without water)94,6365
Polymers94,6365
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Mitochondrial Calcium Uniporter


Mass: 18927.207 Da / Num. of mol.: 5 / Fragment: UNP residues 167-318
Mutation: C170A, C207A, M215A, M222S, M242V, C255A, M313L, F318E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: mcu-1, CELE_K02B2.3, K02B2.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21121

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N TROSY
1142isotropic22D 1H-13C HSQC aliphatic
1153isotropic22D 1H-13C HSQC aliphatic
221isotropic13D tr-HNCA
231isotropic13D tr-HN(CO)CA
241isotropic13D tr-HN(CA)CO
251isotropic13D tr-HNCO
261isotropic13D tr-HN(CA)CB
171isotropic13D 15N-15N HSQC-NOESY-TROSY
182isotropic23D 1H-15N NOESY-TROSY
292isotropic23D 1H-15N NOESY-TROSY
1102isotropic23D 1H-13C Methyl NOESY
2112isotropic23D 1H-13C Methyl NOESY
1123isotropic23D 1H-15N NOESY-TROSY
2133isotropic23D 1H-15N NOESY-TROSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.8 mM [100% 13C; 100% 15N; 85% 2H] MCU-dNTD, 27 mM Foscholine-14, 20 mM MES, 75 mM NaCl, 2 mM EDTA, 0.3 mM NaN3, 95% H2O/5% D2Otriple-labeled sample95% H2O/5% D2O
micelle20.8 mM [100% 13C; 100% 15N] MCU-dNTD, 27 mM [100% 2H at acyl chain] Foscholine-14, 20 mM MES, 75 mM NaCl, 2 mM EDTA, 0.3 mM NaN3, 95% H2O/5% D2Odouble-labeled sample95% H2O/5% D2O
micelle30.4 mM [100% 15N; 100% 2H] MCU-dNTD, 0.4 mM [15% 13C] MCU-dNTD, 27 mM [100% 2H at acyl chain] Foscholine-14, 20 mM MES, 75 mM NaCl, 2 mM EDTA, 0.3 mM NaN3, 95% H2O/5% D2Omixed labeled sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMMCU-dNTD[100% 13C; 100% 15N; 85% 2H]1
27 mMFoscholine-14natural abundance1
20 mMMESnatural abundance1
75 mMNaClnatural abundance1
2 mMEDTAnatural abundance1
0.3 mMNaN3natural abundance1
0.8 mMMCU-dNTD[100% 13C; 100% 15N]2
27 mMFoscholine-14[100% 2H at acyl chain]2
20 mMMESnatural abundance2
75 mMNaClnatural abundance2
2 mMEDTAnatural abundance2
0.3 mMNaN3natural abundance2
0.4 mMMCU-dNTD-1[100% 15N; 100% 2H]3
0.4 mMMCU-dNTD-2[15% 13C]3
27 mMFoscholine-14[100% 2H at acyl chain]3
20 mMMESnatural abundance3
75 mMNaClnatural abundance3
2 mMEDTAnatural abundance3
0.3 mMNaN3natural abundance3
Sample conditions

Ionic strength: 100 mM / Ionic strength err: 10 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature err: 0.2

Conditions-IDLabelTemperature (K)
123C23 C
233C33 C

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II6001cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III9002cryogenic probe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNchemical shift assignment
XEASYBartels et al.chemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
XPLOR-NIHSchwieters et alstructure calculation
XPLOR-NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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