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Yorodumi- EMDB-9945: Intact human mitochondrial calcium uniporter complex with MICU1/M... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9945 | ||||||||||||
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Title | Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | ion channel / mitochondrial Ca2+ uptake / MCU / MICU / TRANSPORT PROTEIN | ||||||||||||
Function / homology | Function and homology information mitochondrial crista junction / positive regulation of cristae formation / 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 / positive regulation of mitochondrial calcium ion concentration ...mitochondrial crista junction / positive regulation of cristae formation / 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 / positive regulation of mitochondrial calcium ion concentration / mitochondrial calcium ion homeostasis / calcium ion sensor activity / channel activator activity / calcium import into the mitochondrion / calcium ion import / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / calcium channel inhibitor activity / calcium channel complex / Mitochondrial protein degradation / calcium-mediated signaling / calcium channel activity / protein homooligomerization / positive regulation of insulin secretion / mitochondrial membrane / mitochondrial intermembrane space / defense response / glucose homeostasis / protein complex oligomerization / protein-macromolecule adaptor activity / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / calcium ion binding / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Zhuo W / Zhou H | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9945.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-9945-v30.xml emd-9945.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
Images | emd_9945.png | 103.5 KB | ||
Filedesc metadata | emd-9945.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9945 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9945 | HTTPS FTP |
-Validation report
Summary document | emd_9945_validation.pdf.gz | 375 KB | Display | EMDB validaton report |
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Full document | emd_9945_full_validation.pdf.gz | 374.6 KB | Display | |
Data in XML | emd_9945_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_9945_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9945 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9945 | HTTPS FTP |
-Related structure data
Related structure data | 6k7yMC 9944C 6k7xC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9945.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Intact human mitochondrial calcium uniporter complex with MICU1/M...
Entire | Name: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits |
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Components |
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-Supramolecule #1: Intact human mitochondrial calcium uniporter complex with MICU1/M...
Supramolecule | Name: Intact human mitochondrial calcium uniporter complex with MICU1/MICU2 subunits type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Calcium uniporter protein, mitochondrial
Macromolecule | Name: Calcium uniporter protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 32.300203 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Essential MCU regulator, mitochondrial
Macromolecule | Name: Essential MCU regulator, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 5.993192 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: VIVTRSGAIL PKPVKMSFGL LRVFSIVIPF LYVGTLISKN FAALLEEHDI FVPE UniProtKB: Essential MCU regulator, mitochondrial |
-Macromolecule #3: Calcium uptake protein 1, mitochondrial
Macromolecule | Name: Calcium uptake protein 1, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 54.432258 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: Calcium uptake protein 2, mitochondrial
Macromolecule | Name: Calcium uptake protein 2, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.852695 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: CARDIOLIPIN
Macromolecule | Name: CARDIOLIPIN / type: ligand / ID: 6 / Number of copies: 8 / Formula: CDL |
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Molecular weight | Theoretical: 1.464043 KDa |
Chemical component information | ChemComp-CDL: |
-Macromolecule #7: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,...
Macromolecule | Name: (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 |
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Molecular weight | Theoretical: 767.132 Da |
Chemical component information | ChemComp-PLX: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: FLEXIBLE FIT | ||||||||
Output model | PDB-6k7y: |