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- PDB-8wg3: mouse TMEM63b in LMNG-CHS micelle -

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Basic information

Entry
Database: PDB / ID: 8wg3
Titlemouse TMEM63b in LMNG-CHS micelle
ComponentsCSC1-like protein 2,Green fluorescent protein
KeywordsLIPID TRANSPORT / Scramblase
Function / homology
Function and homology information


surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / exocytosis / bioluminescence / generation of precursor metabolites and energy / sensory perception of sound / actin cytoskeleton ...surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / exocytosis / bioluminescence / generation of precursor metabolites and energy / sensory perception of sound / actin cytoskeleton / early endosome membrane / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium permeable stress-gated cation channel 1-like / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / CHOLESTEROL HEMISUCCINATE / Green fluorescent protein / CSC1-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMiyata, Y. / Takahashi, K. / Lee, Y. / Sultan, C.S. / Kuribayashi, R. / Takahashi, M. / Hata, K. / Bamba, T. / Izumi, Y. / Liu, K. ...Miyata, Y. / Takahashi, K. / Lee, Y. / Sultan, C.S. / Kuribayashi, R. / Takahashi, M. / Hata, K. / Bamba, T. / Izumi, Y. / Liu, K. / Uemura, T. / Nomura, N. / Iwata, S. / Nagata, S. / Nishizawa, T. / Segawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Mechanosensitive channel TMEM63B functions as a plasma membrane lipid scramblase
Authors: Miyata, Y. / Takahashi, K. / Lee, Y. / Sultan, C.S. / Kuribayashi, R. / Takahashi, M. / Hata, K. / Bamba, T. / Izumi, Y. / Liu, K. / Uemura, T. / Nomura, N. / Iwata, S. / Nagata, S. / Nishizawa, T. / Segawa, K.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSC1-like protein 2,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9805
Polymers126,7591
Non-polymers2,2204
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CSC1-like protein 2,Green fluorescent protein


Mass: 126759.461 Da / Num. of mol.: 1 / Mutation: F64L,S65T,A206K,H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Tmem63b, GFP / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q3TWI9, UniProt: P42212
#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4
#3: Chemical ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse TMEM63B / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human) / Cell: FreeStyle 293-F
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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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 / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4cryoSPARC4.2.1CTF correction
7Coot0.9.9.8model fitting
8ISOLDE1.4.3model fitting
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
14Servalcat0.2.24model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110878 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingAccession code: Q3TWI9 / Source name: AlphaFold / Type: in silico model
RefinementResolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.811 / SU B: 19.951 / SU ML: 0.324 / ESU R: 0.276
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.44152 --
obs0.44152 138849 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 148.666 Å2
Refinement stepCycle: 1 / Total: 4586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0124724
ELECTRON MICROSCOPYr_bond_other_d00.0164582
ELECTRON MICROSCOPYr_angle_refined_deg1.531.6466430
ELECTRON MICROSCOPYr_angle_other_deg0.5121.56410518
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.8345542
ELECTRON MICROSCOPYr_dihedral_angle_2_deg18.132531
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.07410739
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0820.2738
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.025259
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021141
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1714.5292186
ELECTRON MICROSCOPYr_mcbond_other16.99614.5312187
ELECTRON MICROSCOPYr_mcangle_it27.54426.0872722
ELECTRON MICROSCOPYr_mcangle_other27.54326.0892723
ELECTRON MICROSCOPYr_scbond_it15.66315.5122538
ELECTRON MICROSCOPYr_scbond_other15.66115.5132539
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other25.95928.0173709
ELECTRON MICROSCOPYr_long_range_B_refined43.445162.9318297
ELECTRON MICROSCOPYr_long_range_B_other43.444162.9318298
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.647 10207 -
obs--100 %

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