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- PDB-6k7x: Human MCU-EMRE complex -

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Basic information

Entry
Database: PDB / ID: 6k7x
TitleHuman MCU-EMRE complex
Components
  • Calcium uniporter protein, mitochondrial
  • Essential MCU regulator, mitochondrial
KeywordsTRANSPORT PROTEIN / ion channel / Mitochondrial Ca2+ uptake / MCU
Function / homology
Function and homology information


uniporter activity / mitochondrial calcium ion transmembrane transport / uniplex complex / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / channel activator activity / cellular response to calcium ion starvation ...uniporter activity / mitochondrial calcium ion transmembrane transport / uniplex complex / Processing of SMDT1 / positive regulation of mitochondrial calcium ion concentration / Mitochondrial calcium ion transport / mitochondrial calcium ion homeostasis / calcium import into the mitochondrion / channel activator activity / cellular response to calcium ion starvation / positive regulation of neutrophil chemotaxis / positive regulation of mitochondrial fission / protein complex oligomerization / calcium channel complex / Mitochondrial protein degradation / calcium-mediated signaling / positive regulation of insulin secretion / calcium channel activity / glucose homeostasis / protein-macromolecule adaptor activity / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
Similarity search - Function
Essential MCU regulator, mitochondrial / Putative mitochondrial precursor protein / Calcium uniporter protein, C-terminal / MCU family / Mitochondrial calcium uniporter
Similarity search - Domain/homology
CARDIOLIPIN / Chem-PLX / Calcium uniporter protein, mitochondrial / Essential MCU regulator, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
C: Calcium uniporter protein, mitochondrial
A: Calcium uniporter protein, mitochondrial
B: Calcium uniporter protein, mitochondrial
D: Calcium uniporter protein, mitochondrial
H: Essential MCU regulator, mitochondrial
E: Essential MCU regulator, mitochondrial
F: Essential MCU regulator, mitochondrial
G: Essential MCU regulator, mitochondrial
K: Calcium uniporter protein, mitochondrial
L: Calcium uniporter protein, mitochondrial
M: Calcium uniporter protein, mitochondrial
N: Calcium uniporter protein, mitochondrial
O: Essential MCU regulator, mitochondrial
P: Essential MCU regulator, mitochondrial
Q: Essential MCU regulator, mitochondrial
R: Essential MCU regulator, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,57446
Polymers306,34716
Non-polymers24,22730
Water00
1


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

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Components

#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
#3: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: Human MCU-EMRE complex / Type: COMPLEX / Entity ID: #1-#2 / 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 FIELD
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
9PHENIX1.15model refinement
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179468 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00723356
ELECTRON MICROSCOPYf_angle_d1.01731336
ELECTRON MICROSCOPYf_dihedral_angle_d16.23814436
ELECTRON MICROSCOPYf_chiral_restr0.1053460
ELECTRON MICROSCOPYf_plane_restr0.0083784

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