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- EMDB-30495: Cryo-EM structure of human TMEM120A/TACAN -

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Basic information

Entry
Database: EMDB / ID: EMD-30495
TitleCryo-EM structure of human TMEM120A/TACAN
Map data
Sample
  • Complex: Homodimer of human TMEM120A
    • Protein or peptide: MCherry fluorescent protein,Ion channel TACAN
Function / homology
Function and homology information


protein heterooligomerization / nuclear inner membrane / fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / bioluminescence / monoatomic ion transmembrane transport / 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)
Methodsingle 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, 2020-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cxr
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30495.png

Downloads & links

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Map

FileDownload / File: emd_30495.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-3.3260713 - 8.23244
Average (Standard dev.)0.002515657 (±0.08435696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.14 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z239.140239.140239.140
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-3.3268.2320.003

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Supplemental data

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Mask #1

Fileemd_30495_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_30495_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30495_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30495_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimer of human TMEM120A

EntireName: Homodimer of human TMEM120A
Components
  • Complex: Homodimer of human TMEM120A
    • Protein or peptide: MCherry fluorescent protein,Ion channel TACAN

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Supramolecule #1: Homodimer of human TMEM120A

SupramoleculeName: Homodimer of human TMEM120A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anaplasma marginale (bacteria)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: MCherry fluorescent protein,Ion channel TACAN

MacromoleculeName: MCherry fluorescent protein,Ion channel TACAN / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.643555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SDEVDAMVSK GEEDNMAIIK EFMRFKVHME GSVNGHEFEI EGEGEGRPYE GTQTAKLKV TKGGPLPFAW DILSPQFMYG SKAYVKHPAD IPDYLKLSFP EGFKWERVMN FEDGGVVTVT QDSSLQDGEF I YKVKLRGT ...String:
MDYKDDDDKG SDYKDDDDKG SDYKDDDDKG SDEVDAMVSK GEEDNMAIIK EFMRFKVHME GSVNGHEFEI EGEGEGRPYE GTQTAKLKV TKGGPLPFAW DILSPQFMYG SKAYVKHPAD IPDYLKLSFP EGFKWERVMN FEDGGVVTVT QDSSLQDGEF I YKVKLRGT NFPSDGPVMQ KKTMGWEASS ERMYPEDGAL KGEIKQRLKL KDGGHYDAEV KTTYKAKKPV QLPGAYNVNI KL DITSHNE DYTIVEQYER AEGRHSTGGM DELYKLEVLF QGPEFMQPPP PGPLGDCLRD WEDLQQDFQN IQETHRLYRL KLE ELTKLQ NNCTSSITRQ KKRLQELALA LKKCKPSLPA EAEGAAQELE NQMKERQGLF FDMEAYLPKK NGLYLSLVLG NVNV TLLSK QAKFAYKDEY EKFKLYLTII LILISFTCRF LLNSRVTDAA FNFLLVWYYC TLTIRESILI NNGSRIKGWW VFHHY VSTF LSGVMLTWPD GLMYQKFRNQ FLSFSMYQSF VQFLQYYYQS GCLYRLRALG ERHTMDLTVE GFQSWMWRGL TFLLPF LFF GHFWQLFNAL TLFNLAQDPQ CKEWQVLMCG FPFLLLFLGN FFTTLRVVHH KFHSQRHGSK KD

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab Initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79080

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