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- PDB-6k7y: Intact human mitochondrial calcium uniporter complex with MICU1/M... -

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Basic information

Entry
Database: PDB / ID: 6k7y
TitleIntact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
Components
  • (Calcium uptake protein ...) x 2
  • Calcium uniporter protein, mitochondrial
  • Essential MCU regulator, mitochondrial
KeywordsTRANSPORT PROTEIN / ion channel / mitochondrial Ca2+ uptake / MCU / MICU
Function / homology
Function and homology information


negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis ...negative regulation of mitochondrial calcium ion concentration / regulation of cellular hyperosmotic salinity response / uniporter activity / Processing of SMDT1 / mitochondrial calcium ion transmembrane transport / uniplex complex / calcium import into the mitochondrion / Mitochondrial calcium ion transport / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / calcium channel complex / calcium-mediated signaling / mitochondrial membrane / calcium channel activity / protein homooligomerization / defense response / mitochondrial intermembrane space / positive regulation of insulin secretion / glucose homeostasis / protein complex oligomerization / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / calcium ion binding / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Essential MCU regulator, mitochondrial / Putative mitochondrial precursor protein / Calcium uptake protein 1/2/3 / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Essential MCU regulator, mitochondrial / Putative mitochondrial precursor protein / Calcium uptake protein 1/2/3 / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
CARDIOLIPIN / Chem-PLX / Calcium uptake protein 2, mitochondrial / Calcium uniporter protein, mitochondrial / Calcium uptake protein 1, mitochondrial / Essential MCU regulator, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhuo, W. / Zhou, H. / Yang, M.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21532004 China
National Science Foundation (NSF, China)31570733 China
National Science Foundation (NSF, China)31900857 China
CitationJournal: Protein Cell / Year: 2021
Title: Structure of intact human MCU supercomplex with the auxiliary MICU subunits.
Authors: Wei Zhuo / Heng Zhou / Runyu Guo / Jingbo Yi / Laixing Zhang / Lei Yu / Yinqiang Sui / Wenwen Zeng / Peiyi Wang / Maojun Yang /
History
DepositionJun 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Calcium uniporter protein, mitochondrial
B: Calcium uniporter protein, mitochondrial
C: Calcium uniporter protein, mitochondrial
D: Calcium uniporter protein, mitochondrial
E: Essential MCU regulator, mitochondrial
F: Essential MCU regulator, mitochondrial
G: Essential MCU regulator, mitochondrial
H: Essential MCU regulator, mitochondrial
I: Calcium uptake protein 1, mitochondrial
J: Calcium uptake protein 2, mitochondrial
N: Calcium uniporter protein, mitochondrial
O: Calcium uniporter protein, mitochondrial
P: Calcium uniporter protein, mitochondrial
Q: Calcium uniporter protein, mitochondrial
R: Essential MCU regulator, mitochondrial
S: Essential MCU regulator, mitochondrial
T: Essential MCU regulator, mitochondrial
U: Essential MCU regulator, mitochondrial
V: Calcium uptake protein 1, mitochondrial
W: Calcium uptake protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,98446
Polymers494,91720
Non-polymers24,06726
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 16 molecules ABCDNOPQEFGHRSTU

#1: Protein
Calcium uniporter protein, mitochondrial / HsMCU / Coiled-coil domain-containing protein 109A


Mass: 32300.203 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCU, C10orf42, CCDC109A / Production host: Homo sapiens (human) / References: UniProt: Q8NE86
#2: Protein
Essential MCU regulator, mitochondrial / Single-pass membrane protein with aspartate-rich tail 1 / mitochondrial


Mass: 5993.192 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMDT1, C22orf32, EMRE / Production host: Homo sapiens (human) / References: UniProt: Q9H4I9

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Calcium uptake protein ... , 2 types, 4 molecules IVJW

#3: Protein Calcium uptake protein 1, mitochondrial / Atopy-related autoantigen CALC / ara CALC / Calcium-binding atopy-related autoantigen 1


Mass: 54432.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU1, CALC, CBARA1 / Production host: Homo sapiens (human) / References: UniProt: Q9BPX6
#4: Protein Calcium uptake protein 2, mitochondrial / EF-hand domain-containing family member A1


Mass: 39852.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICU2, EFHA1 / Production host: Homo sapiens (human) / References: UniProt: Q8IYU8

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Non-polymers , 3 types, 26 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#7: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15_3459: / Classification: refinement
EM software
IDNameVersionCategory
12RELION33D reconstruction
13PHENIX1.15model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91728 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16K7X

6k7x

16K7X1PDBexperimental model
24NSC

4nsc

14NSC2PDBexperimental model
36AGH

6agh

16AGH3PDBexperimental model
RefinementHighest resolution: 3.6 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00533566
ELECTRON MICROSCOPYf_angle_d0.64345022
ELECTRON MICROSCOPYf_dihedral_angle_d15.85820564
ELECTRON MICROSCOPYf_chiral_restr0.0754950
ELECTRON MICROSCOPYf_plane_restr0.0045546

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