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- PDB-7cxr: Cryo-EM structure of human TMEM120A/TACAN -

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Basic information

Entry
Database: PDB / ID: 7cxr
TitleCryo-EM structure of human TMEM120A/TACAN
ComponentsMCherry fluorescent protein,Ion channel TACAN
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


protein heterooligomerization / nuclear inner membrane / fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transmembrane transport / bioluminescence / generation of precursor metabolites and energy / protein homooligomerization / monoatomic ion channel activity / membrane / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMPIT-like protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Ion channel TACAN / MCherry fluorescent protein
Similarity search - Component
Biological speciesAnaplasma marginale (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsYan, Z. / Wu, J. / Ke, M.
CitationJournal: Cell Discov / Year: 2021
Title: Cryo-EM structures of human TMEM120A and TMEM120B.
Authors: Meng Ke / Yue Yu / Changjian Zhao / Shirong Lai / Qiang Su / Weidan Yuan / Lina Yang / Dong Deng / Kun Wu / Weizheng Zeng / Jia Geng / Jianping Wu / Zhen Yan /
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: MCherry fluorescent protein,Ion channel TACAN
B: MCherry fluorescent protein,Ion channel TACAN


Theoretical massNumber of molelcules
Total (without water)145,2872
Polymers145,2872
Non-polymers00
Water0
1


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

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Components

#1: Protein MCherry fluorescent protein,Ion channel TACAN / Transmembrane protein 120A / Transmembrane protein induced by tumor necrosis factor alpha / TMEM120A/TACAN


Mass: 72643.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma marginale (bacteria), (gene. exp.) Homo sapiens (human)
Gene: mCherry, TMEM120A, TACAN, TMPIT / Production host: Homo sapiens (human) / References: UniProt: X5DSL3, UniProt: Q9BXJ8

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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: Homodimer of human TMEM120A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Anaplasma marginale (bacteria)770
21Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79080 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0075316
ELECTRON MICROSCOPYf_angle_d0.7627180
ELECTRON MICROSCOPYf_dihedral_angle_d20.247666
ELECTRON MICROSCOPYf_chiral_restr0.044766
ELECTRON MICROSCOPYf_plane_restr0.004892

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