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- PDB-7d60: Cryo-EM Structure of human CALHM5 in the presence of rubidium red -

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Basic information

Entry
Database: PDB / ID: 7d60
TitleCryo-EM Structure of human CALHM5 in the presence of rubidium red
ComponentsCalcium homeostasis modulator protein 5
KeywordsTRANSPORT PROTEIN / large pore channel
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / plasma membrane / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE / Calcium homeostasis modulator protein 5
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsLiu, J. / Guan, F.H. / Wu, J. / Wan, F.T. / Lei, M. / Ye, S.
Funding support China, 8items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)31525001 China
National Natural Science Foundation of China (NSFC)31971127 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)31900041 China
National Natural Science Foundation of China (NSFC)31525007 China
National Natural Science Foundation of China (NSFC)31930063 China
CitationJournal: Cell Discov / Year: 2020
Title: Cryo-EM structures of human calcium homeostasis modulator 5.
Authors: Jie Liu / Futang Wan / Qiuheng Jin / Xiaoxiao Li / Eijaz Ahmed Bhat / Jiangtao Guo / Ming Lei / Fenghui Guan / Jian Wu / Sheng Ye /
History
DepositionSep 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Calcium homeostasis modulator protein 5
B: Calcium homeostasis modulator protein 5
C: Calcium homeostasis modulator protein 5
D: Calcium homeostasis modulator protein 5
E: Calcium homeostasis modulator protein 5
F: Calcium homeostasis modulator protein 5
G: Calcium homeostasis modulator protein 5
H: Calcium homeostasis modulator protein 5
I: Calcium homeostasis modulator protein 5
J: Calcium homeostasis modulator protein 5
K: Calcium homeostasis modulator protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,42566
Polymers362,13411
Non-polymers23,29055
Water00
1


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

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Components

#1: Protein
Calcium homeostasis modulator protein 5 / Protein FAM26E


Mass: 32921.305 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM5, C6orf188, FAM26E / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q8N5C1
#2: Chemical...
ChemComp-PA8 / 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 423.458 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C19H36O8P
Has ligand of interestN
Has protein modificationY

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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: Calcium homeostasis modulator protein 5 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human) / Cellular location: membrane
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 / Plasmid: pEZT
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding 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 K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 576663 / Symmetry type: POINT

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