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- EMDB-37502: mouse TMEM63b in DDM-CHS micelle with YN9303-24 Fab -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37502
Titlemouse TMEM63b in DDM-CHS micelle with YN9303-24 Fab
Map datasharpened map
Sample
  • Complex: mouse TMEM63B
    • Protein or peptide: CSC1-like protein 2,Green fluorescent protein
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsScramblase / LIPID TRANSPORT
Function / homology
Function and homology information


alveolar lamellar body membrane / 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 ...alveolar lamellar body membrane / 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
Green fluorescent protein / CSC1-like protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMiyata Y / Takahashi K / Lee Y / Sultan CS / Kuribayashi R / Takahashi M / Hata K / Bamba T / Izumi Y / Liu K ...Miyata Y / Takahashi K / Lee Y / Sultan CS / 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, 1 items
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 CS / 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, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37502.png

Downloads & links

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Map

FileDownload / File: emd_37502.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 160 pix.
= 249. Å		1.56 Å/pix.
x 160 pix.
= 249. Å		1.56 Å/pix.
x 160 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.55625 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.481
Minimum - Maximum-2.399473 - 3.3892274
Average (Standard dev.)0.0036068037 (±0.066766575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37502_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_37502_msk_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: halfmapA

Fileemd_37502_half_map_1.map
AnnotationhalfmapA
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: halfmapB

Fileemd_37502_half_map_2.map
AnnotationhalfmapB
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : mouse TMEM63B

EntireName: mouse TMEM63B
Components
  • Complex: mouse TMEM63B
    • Protein or peptide: CSC1-like protein 2,Green fluorescent protein
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: mouse TMEM63B

SupramoleculeName: mouse TMEM63B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 100 KDa

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

MacromoleculeName: CSC1-like protein 2,Green fluorescent protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 126.759461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPFLLATLG TAALNSSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERERV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGF(P1L)SWL TAIFRIKDDE IRDKCGGDAV HYLSFQR HI IGLLVVVGVL ...String:
MLPFLLATLG TAALNSSNPK DYCYSARIRS TVLQGLPFGG VPTVLALDFM CFLALLFLFS ILRKVAWDYG RLALVTDADR LRRQERERV EQEYVASAMH GDSHDRYERL TSVSSSVDFD QRDNGF(P1L)SWL TAIFRIKDDE IRDKCGGDAV HYLSFQR HI IGLLVVVGVL SVGIVLPVNF SGDLLENNAY SFGRTTIANL KSGNNLLWLH TSFAFLYLLL TVYSMRRHTS KMRYKEDD L VKRTLFINGI SKYAESEKIK KHFEEAYPNC TVLEARPCYN VARLMFLDAE RKKAERGKLY FTNLQSKENV PAMINPKPC GHLCCCVVRG CEQVEAIEYY TKLEQRLKED YRREKEKVNE KPLGMAFVTF HNETITAIIL KDFNVCKCQG CTCRGEPRAS SCSEALHIS NWTVTYAPDP QNIYWEHLSI RGFIWWLRCL VINVVLFILL FFLTTPAIII TTMDKFNVTK PVEYLNNPII T QFFPTLLL WCFSALLPTI VYYSAFFEAH WTRSGENRTT MHKCYTFLIF MVLLLPSLGL SSLDLFFRWL FDKKFLAEAA IR FECVFLP DNGAFFVNYV IASAFIGNAM DLLRIPGLLM YMIRLCLARS AAERRNVKRH QAYEFQFGAA YAWMMCVFTV VMT YSITCP IIVPFGLMYM LLKHLVDRYN LYYAYLPAKL DKKIHSGAVN QVVAAPILCL FWLLFFSTMR TGFLAPTSMF TFVV LVITI VICLCHVCFG HFKYLSAHNY KIEHTETDAV SSRSNGRPPT AGAVPKSAKY IAQVLQDSEG DGDGDGAPGS SGDEP PSSS SQDEELLMPP DGLTDTDFQS CEDSLIENEI HQGTENLYFQ GSAAAAVSKG EELFTGVVPI LVELDGDVNG HKFSVS GEG EGDATYGKLT LKFICTTGKL PVPWPTLVTT LTYGVQCFSR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRA EV KFEGDTLVNR IELKGIDFKE DGNILGHKLE YNYNSHNVYI MADKQKNGIK VNFKIRHNIE DGSVQLADHY QQNTPIGD G PVLLPDNHYL STQSKLSKDP NEKRDHMVLL EFVTAAGITL GMDELYKSGL RSWSHPQFEK GGGSGGGSGG SAWSHPQFE K

UniProtKB: CSC1-like protein 2, Green fluorescent protein

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Macromolecule #2: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / Number of copies: 1 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 456579
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

twi9


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8wg4:
mouse TMEM63b in DDM-CHS micelle with YN9303-24 Fab

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