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Open data
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Basic information
Entry | Database: PDB / ID: 8kb4 | ||||||
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Title | Cryo-EM structure of human TMEM87A A308M | ||||||
![]() | Transmembrane protein 87A,EGFP | ||||||
![]() | MEMBRANE PROTEIN / non-selective cation channel / ion channel / Golgi-localized protein | ||||||
Function / homology | ![]() detection of mechanical stimulus involved in sensory perception of touch / retrograde transport, endosome to Golgi / Golgi cisterna membrane / bioluminescence / RHOA GTPase cycle / generation of precursor metabolites and energy / ruffle / cellular response to mechanical stimulus / Golgi membrane / Golgi apparatus ...detection of mechanical stimulus involved in sensory perception of touch / retrograde transport, endosome to Golgi / Golgi cisterna membrane / bioluminescence / RHOA GTPase cycle / generation of precursor metabolites and energy / ruffle / cellular response to mechanical stimulus / Golgi membrane / Golgi apparatus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Han, A. / Kim, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of human TMEM87A, PE-bound Authors: Han, A. / Kim, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 68.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 31.8 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37069MC ![]() 8hsiC ![]() 8httC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 96983.539 Da / Num. of mol.: 1 / Mutation: A308M Source method: isolated from a genetically manipulated source Details: Transmembrane protein 87A A308M with GFP and twin strep tag Source: (gene. exp.) ![]() ![]() ![]() Gene: TMEM87A / Cell (production host): Expi293F / Cell line (production host): HEK293F / Production host: ![]() | ||||
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#2: Sugar | #3: Chemical | ChemComp-65I / ( | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Transmembrane protein 87A A308M with GFP tag and Twin-strep tag Type: ORGANELLE OR CELLULAR COMPONENT Details: Transmembrane protein 87A A308M with GFP tag and Twin-strep tag purified with detergent LMNG/CHS Entity ID: #1 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 9 Details: 50mM HEPES pH 7.5, 250mM NaCl, 0.01% (w/v) LMNG, 0.002% (w/v) CHS | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse | |||||||||||||||||||||||||
Specimen support | Details: The grid was negatively glow-discharged for 60 sec with 15mA | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Using Zemlin tableau in sherpa |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 58900 X / Nominal defocus max: 1900 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Residual tilt: 10 mradians |
Image recording | Average exposure time: 6.09 sec. / Electron dose: 67.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4565 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Details: PatchCTF in Cryosparc was used / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8101104 Details: 96,330 particles were first picked using a blob picker of cryoSPARC. 2D class average images were generated as templates for subsequent reference-based auto-picking. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 360876 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 40 / Protocol: RIGID BODY FIT / Space: REAL Details: Chimera Fit in map tool was used for initial local fitting. Then, Real-space refinement with the rigid body option in PHENIX was used for flexible fitting. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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