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- EMDB-22216: MCU holocomplex in Low-calcium blocking state -

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Basic information

Entry
Database: EMDB / ID: EMD-22216
TitleMCU holocomplex in Low-calcium blocking state
Map dataMCU holocomplex in Low-calcium blocking state
Sample
  • Complex: MCU/EMRE/MICU1/MICU2 complex
    • 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
Keywordsion channel / 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 / 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
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: 4.6 Å
AuthorsWang Y / Jiang Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2020
Title: Structural insights into the Ca-dependent gating of the human mitochondrial calcium uniporter.
Authors: Yan Wang / Yan Han / Ji She / Nam X Nguyen / Vamsi K Mootha / Xiao-Chen Bai / Youxing Jiang /
Abstract: Mitochondrial Ca uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, ...Mitochondrial Ca uptake is mediated by an inner mitochondrial membrane protein called the mitochondrial calcium uniporter. In humans, the uniporter functions as a holocomplex consisting of MCU, EMRE, MICU1 and MICU2, among which MCU and EMRE form a subcomplex and function as the conductive channel while MICU1 and MICU2 are EF-hand proteins that regulate the channel activity in a Ca-dependent manner. Here, we present the EM structures of the human mitochondrial calcium uniporter holocomplex (uniplex) in the presence and absence of Ca, revealing distinct Ca dependent assembly of the uniplex. Our structural observations suggest that Ca changes the dimerization interaction between MICU1 and MICU2, which in turn determines how the MICU1-MICU2 subcomplex interacts with the MCU-EMRE channel and, consequently, changes the distribution of the uniplex assemblies between the blocked and unblocked states.
History
DepositionJun 24, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xjx
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22216.png

Downloads & links

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Map

FileDownload / File: emd_22216.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMCU holocomplex in Low-calcium blocking state
Voxel sizeX=Y=Z: 1.666 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.04
Minimum - Maximum-0.053597312 - 0.1520746
Average (Standard dev.)0.0008046618 (±0.0073339297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 266.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6661.6661.666
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z266.560266.560266.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0540.1520.001

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Supplemental data

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Sample components

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Entire : MCU/EMRE/MICU1/MICU2 complex

EntireName: MCU/EMRE/MICU1/MICU2 complex
Components
  • Complex: MCU/EMRE/MICU1/MICU2 complex
    • 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

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Supramolecule #1: MCU/EMRE/MICU1/MICU2 complex

SupramoleculeName: MCU/EMRE/MICU1/MICU2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: low calcium blocking state
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 529 KDa

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Macromolecule #1: Calcium uniporter protein, mitochondrial

MacromoleculeName: Calcium uniporter protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.920828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAAAGRSLL LLLSSRGGGG GGAGGCGALT AGCFPGLGVS RHRQQQHHRT VHQRIASWQN LGAVYCSTVV PSDDVTVVYQ NGLPVISVR LPSRRERCQF TLKPISDSVG VFLRQLQEED RGIDRVAIYS PDGVRVAAST GIDLLLLDDF KLVINDLTYH V RPPKRDLL ...String:
MAAAAGRSLL LLLSSRGGGG GGAGGCGALT AGCFPGLGVS RHRQQQHHRT VHQRIASWQN LGAVYCSTVV PSDDVTVVYQ NGLPVISVR LPSRRERCQF TLKPISDSVG VFLRQLQEED RGIDRVAIYS PDGVRVAAST GIDLLLLDDF KLVINDLTYH V RPPKRDLL SHENAATLND VKTLVQQLYT TLCIEQHQLN KERELIERLE DLKEQLAPLE KVRIEISRKA EKRTTLVLWG GL AYMATQF GILARLTWWE YSWDIMEPVT YFITYGSAMA MYAYFVMTRQ EYVYPEARDR QYLLFFHKGA KKSRFDLEKY NQL KDAIAQ AEMDLKRLRD PLQVHLPLRQ IGEKD

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: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.45414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MASGAARWLV LAPVRSGALR SGPSLRKDGD VSAAWSGSGR SLVPSRSVIV TRSGAILPKP VKMSFGLLRV FSIVIPFLYV GTLISKNFA ALLEEHDIFV PEDDDDDD

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.432258 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.742141 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAAAAGSCAR VAAWGGKLRR GLAVSRQAVR SPGPLAAAVA GAALAGAGAA WHHSRVSVAA RDGSFTVSAQ KNVEHGIIYI GKPSLRKQR FMQFSSLEHE GEYYMTPRDF LFSVMFEQME RKTSVKKLTK KDIEDTLSGI QTAGCGSTFF RDLGDKGLIS Y TEYLFLLT ...String:
MAAAAGSCAR VAAWGGKLRR GLAVSRQAVR SPGPLAAAVA GAALAGAGAA WHHSRVSVAA RDGSFTVSAQ KNVEHGIIYI GKPSLRKQR FMQFSSLEHE GEYYMTPRDF LFSVMFEQME RKTSVKKLTK KDIEDTLSGI QTAGCGSTFF RDLGDKGLIS Y TEYLFLLT ILTKPHSGFH VAFKMLDTDG NEMIEKREFF KLQKIISKQD DLMTVKTNET GYQEAIVKEP EINTTLQMRF FG KRGQRKL HYKEFRRFME NLQTEIQEME FLQFSKGLSF MRKEDFAEWL LFFTNTENKD IYWKNVREKL SAGESISLDE FKS FCHFTT HLEDFAIAMQ MFSLAHRPVR LAEFKRAVKV ATGQELSNNI LDTVFKIFDL DGDECLSHEE FLGVLKNRMH RGLW VPQHQ SIQEYWKCVK KESIKGVKEV WKQAGKGLF

UniProtKB: Calcium uptake protein 2, mitochondrial

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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

Concentration1.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging.
DetailsThis sample was reconstituted in Msp1 nanodiscs

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 30.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120792

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