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- EMDB-9945: Intact human mitochondrial calcium uniporter complex with MICU1/M... -

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Basic information

Entry
Database: EMDB / ID: EMD-9945
TitleIntact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
Map data
Sample
  • Complex: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
    • Protein or peptide: Calcium uniporter protein, mitochondrial
    • Protein or peptide: Essential MCU regulator, mitochondrial
    • Protein or peptide: Calcium uptake protein 1, mitochondrial
    • Protein or peptide: Calcium uptake protein 2, mitochondrial
  • Ligand: CALCIUM ION
  • Ligand: CARDIOLIPIN
  • Ligand: (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
Keywordsion channel / mitochondrial Ca2+ uptake / MCU / MICU / TRANSPORT PROTEIN
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 / Mitochondrial calcium ion transport / calcium import into the mitochondrion / 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 / Mitochondrial calcium ion transport / calcium import into the mitochondrion / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion import / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / Mitochondrial protein degradation / calcium channel complex / mitochondrial membrane / calcium-mediated signaling / calcium channel activity / protein homooligomerization / positive regulation of insulin secretion / mitochondrial intermembrane space / defense response / protein complex oligomerization / glucose homeostasis / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhuo W / Zhou H
Funding support China, 3 items
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, 2019-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6k7y
  • Surface level: 12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9945.png

Downloads & links

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Map

FileDownload / File: emd_9945.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 360 pix.
= 392.76 Å		1.09 Å/pix.
x 360 pix.
= 392.76 Å		1.09 Å/pix.
x 360 pix.
= 392.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0 / Movie #1: 12
Minimum - Maximum-39.141677999999999 - 78.091064000000003
Average (Standard dev.)0.10311705 (±1.8371305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.75998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z392.760392.760392.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-39.14278.0910.103

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Supplemental data

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Sample components

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Entire : Intact human mitochondrial calcium uniporter complex with MICU1/M...

EntireName: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
Components
  • Complex: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
    • Protein or peptide: Calcium uniporter protein, mitochondrial
    • Protein or peptide: Essential MCU regulator, mitochondrial
    • Protein or peptide: Calcium uptake protein 1, mitochondrial
    • Protein or peptide: Calcium uptake protein 2, mitochondrial
  • Ligand: CALCIUM ION
  • Ligand: CARDIOLIPIN
  • Ligand: (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

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Supramolecule #1: Intact human mitochondrial calcium uniporter complex with MICU1/M...

SupramoleculeName: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium uniporter protein, mitochondrial

MacromoleculeName: Calcium uniporter protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.300203 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DDVTVVYQNG LPVISVRLPS RRERCQFTLK PISDSVGVFL RQLQEEDRGI DRVAIYSPDG VRVAASTGID LLLLDDFKLV INDLTYHVR PPKRDLLSHE NAATLNDVKT LVQQLYTTLC IEQHQLNKER ELIERLEDLK EQLAPLEKVR IEISRKAEKR T TLVLWGGL ...String:
DDVTVVYQNG LPVISVRLPS RRERCQFTLK PISDSVGVFL RQLQEEDRGI DRVAIYSPDG VRVAASTGID LLLLDDFKLV INDLTYHVR PPKRDLLSHE NAATLNDVKT LVQQLYTTLC IEQHQLNKER ELIERLEDLK EQLAPLEKVR IEISRKAEKR T TLVLWGGL AYMATQFGIL ARLTWWEYSW DIMEPVTYFI TYGSAMAMYA YFVMTRQEYV YPEARDRQYL LFFHKGAKKS RF DLEKYNQ LKDAIAQAEM DLKRLRDPLQ VHLPLRQIG

UniProtKB: Calcium uniporter protein, mitochondrial

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Macromolecule #2: Essential MCU regulator, mitochondrial

MacromoleculeName: Essential MCU regulator, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.993192 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VIVTRSGAIL PKPVKMSFGL LRVFSIVIPF LYVGTLISKN FAALLEEHDI FVPE

UniProtKB: Essential MCU regulator, mitochondrial

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Macromolecule #3: Calcium uptake protein 1, mitochondrial

MacromoleculeName: Calcium uptake protein 1, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.432258 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFRLNSLSAL AELAVGSRWY HGGSQPIQIR RRLMMVAFLG ASAVTASTGL LWKRAHAESP PCVDNLKSDI GDKGKNKDEG DVCNHEKKT ADLAPHPEEK KKKRSGFRDR KVMEYENRIR AYSTPDKIFR YFATLKVISE PGEAEVFMTP EDFVRSITPN E KQPEHLGL ...String:
MFRLNSLSAL AELAVGSRWY HGGSQPIQIR RRLMMVAFLG ASAVTASTGL LWKRAHAESP PCVDNLKSDI GDKGKNKDEG DVCNHEKKT ADLAPHPEEK KKKRSGFRDR KVMEYENRIR AYSTPDKIFR YFATLKVISE PGEAEVFMTP EDFVRSITPN E KQPEHLGL DQYIIKRFDG KKISQEREKF ADEGSIFYTL GECGLISFSD YIFLTTVLST PQRNFEIAFK MFDLNGDGEV DM EEFEQVQ SIIRSQTSMG MRHRDRPTTG NTLKSGLCSA LTTYFFGADL KGKLTIKNFL EFQRKLQHDV LKLEFERHDP VDG RITERQ FGGMLLAYSG VQSKKLTAMQ RQLKKHFKEG KGLTFQEVEN FFTFLKNIND VDTALSFYHM AGASLDKVTM QQVA RTVAK VELSDHVCDV VFALFDCDGN GELSNKEFVS IMKQRLMRGL EKPKDMGFTR LMQAMWKCAQ ETAWDFALPK Q

UniProtKB: Calcium uptake protein 1, mitochondrial

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Macromolecule #4: Calcium uptake protein 2, mitochondrial

MacromoleculeName: Calcium uptake protein 2, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.852695 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PSLRKQRFMQ FSSLEHEGEY YMTPRDFLFS VMFEQMERKT SVKKLTKKDI EDTLSGIQTA GCGSTFFRDL GDKGLISYTE YLFLLTILT KPHSGFHVAF KMLDTDGNEM IEKREFFKLQ KIISKQDDLM TVKTNETGYQ EAIVKEPEIN TTLQMRFFGK R GQRKLHYK ...String:
PSLRKQRFMQ FSSLEHEGEY YMTPRDFLFS VMFEQMERKT SVKKLTKKDI EDTLSGIQTA GCGSTFFRDL GDKGLISYTE YLFLLTILT KPHSGFHVAF KMLDTDGNEM IEKREFFKLQ KIISKQDDLM TVKTNETGYQ EAIVKEPEIN TTLQMRFFGK R GQRKLHYK EFRRFMENLQ TEIQEMEFLQ FSKGLSFMRK EDFAEWLLFF TNTENKDIYW KNVREKLSAG ESISLDEFKS FC HFTTHLE DFAIAMQMFS LAHRPVRLAE FKRAVKVATG QELSNNILDT VFKIFDLDGD ECLSHEEFLG VLKNRMHRGL WVP QHQSIQ EYWKCVKKES

UniProtKB: Calcium uptake protein 2, mitochondrial

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 6 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #7: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...

MacromoleculeName: (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
type: ligand / ID: 7 / Number of copies: 16 / Formula: PLX
Molecular weightTheoretical: 767.132 Da
Chemical component information

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 / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

9944

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 91728
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

6k7x

source_name: PDB, initial_model_type: experimental model

4nsc

source_name: PDB, initial_model_type: experimental model

6agh

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6k7y:
Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits

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