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- PDB-6ytv: Cryo-EM structure of decameric human CALHM6 in the presence of Ca2+ -

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Basic information

Entry
Database: PDB / ID: 6ytv
TitleCryo-EM structure of decameric human CALHM6 in the presence of Ca2+
ComponentsCalcium homeostasis modulator protein 6
KeywordsMEMBRANE PROTEIN / calcium homeostasis modulator / ion channel / placenta
Function / homologyCalcium homeostasis modulator protein 6 / Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator protein 6
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å
AuthorsSawicka, M. / Drozdzyk, K. / Dutzler, R.
Funding support1items
OrganizationGrant numberCountry
Swiss National Science Foundation
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structures and functional properties of CALHM channels of the human placenta.
Authors: Katarzyna Drożdżyk / Marta Sawicka / Maria-Isabel Bahamonde-Santos / Zaugg Jonas / Dawid Deneka / Christiane Albrecht / Raimund Dutzler /
Abstract: The transport of substances across the placenta is essential for the development of the fetus. Here, we were interested in the role of channels of the calcium homeostasis modulator (CALHM) family in ...The transport of substances across the placenta is essential for the development of the fetus. Here, we were interested in the role of channels of the calcium homeostasis modulator (CALHM) family in the human placenta. By transcript analysis, we found the paralogs CALHM2, 4, and 6 to be highly expressed in this organ and upregulated during trophoblast differentiation. Based on electrophysiology, we observed that activation of these paralogs differs from the voltage- and calcium-gated channel CALHM1. Cryo-EM structures of CALHM4 display decameric and undecameric assemblies with large cylindrical pore, while in CALHM6 a conformational change has converted the pore shape into a conus that narrows at the intracellular side, thus describing distinct functional states of the channel. The pore geometry alters the distribution of lipids, which occupy the cylindrical pore of CALHM4 in a bilayer-like arrangement whereas they have redistributed in the conical pore of CALHM6 with potential functional consequences.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Calcium homeostasis modulator protein 6
B: Calcium homeostasis modulator protein 6
C: Calcium homeostasis modulator protein 6
D: Calcium homeostasis modulator protein 6
E: Calcium homeostasis modulator protein 6
F: Calcium homeostasis modulator protein 6
G: Calcium homeostasis modulator protein 6
H: Calcium homeostasis modulator protein 6
I: Calcium homeostasis modulator protein 6
J: Calcium homeostasis modulator protein 6


Theoretical massNumber of molelcules
Total (without water)344,94110
Polymers344,94110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area51760 Å2
ΔGint-518 kcal/mol
Surface area137170 Å2
MethodPISA

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Components

#1: Protein
Calcium homeostasis modulator protein 6 / Protein FAM26F


Mass: 34494.109 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM6, C6orf187, FAM26F / Production host: Homo sapiens (human) / References: UniProt: Q5R3K3

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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: Decameric CALHM6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C10 (10 fold cyclic)
3D reconstructionResolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98104 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00420010
ELECTRON MICROSCOPYf_angle_d0.77427200
ELECTRON MICROSCOPYf_dihedral_angle_d22.5962690
ELECTRON MICROSCOPYf_chiral_restr0.0433170
ELECTRON MICROSCOPYf_plane_restr0.0053350

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