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- EMDB-30587: Cryo-EM Structure of human CALHM5 in the presence of EDTA -

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Basic information

Entry
Database: EMDB / ID: EMD-30587
TitleCryo-EM Structure of human CALHM5 in the presence of EDTA
Map data
Sample
  • Organelle or cellular component: Calcium homeostasis modulator protein 5
    • Protein or peptide: Calcium homeostasis modulator protein 5
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE
Keywordslarge pore channel / TRANSPORT PROTEIN
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator protein 5
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLiu J / Guan FH
Funding support China, 8 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
National Natural Science Foundation of China (NSFC)31525001 China
National Natural Science Foundation of China (NSFC)31971127 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)31900041 China
National Natural Science Foundation of China (NSFC)31525007 China
National Natural Science Foundation of China (NSFC)31930063 China
CitationJournal: Cell Discov / Year: 2020
Title: Cryo-EM structures of human calcium homeostasis modulator 5.
Authors: Jie Liu / Futang Wan / Qiuheng Jin / Xiaoxiao Li / Eijaz Ahmed Bhat / Jiangtao Guo / Ming Lei / Fenghui Guan / Jian Wu / Sheng Ye /
History
DepositionSep 28, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d61
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30587.png

Downloads & links

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Map

FileDownload / File: emd_30587.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.069106214 - 0.14175229
Average (Standard dev.)0.0000048659313 (±0.0036602968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-0.0690.1420.000

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Supplemental data

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Sample components

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Entire : Calcium homeostasis modulator protein 5

EntireName: Calcium homeostasis modulator protein 5
Components
  • Organelle or cellular component: Calcium homeostasis modulator protein 5
    • Protein or peptide: Calcium homeostasis modulator protein 5
  • Ligand: 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: Calcium homeostasis modulator protein 5

SupramoleculeName: Calcium homeostasis modulator protein 5 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human) / Location in cell: membrane

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Macromolecule #1: Calcium homeostasis modulator protein 5

MacromoleculeName: Calcium homeostasis modulator protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.921305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAFQGILKF FLNQKTVIGY SFMALLTVGS ERLFSVVAFK CPCSTENMTY GLVFLFAPAW VLLILGFFLN NRSWRLFTGC CVNPRKIFP RGHSCRFFYV LGQITLSSLV APVMWLSVAL LNGTFYECAM SGTRSSGLLE LICKGKPKEC WEELHKVSCG K TSMLPTVN ...String:
MDAFQGILKF FLNQKTVIGY SFMALLTVGS ERLFSVVAFK CPCSTENMTY GLVFLFAPAW VLLILGFFLN NRSWRLFTGC CVNPRKIFP RGHSCRFFYV LGQITLSSLV APVMWLSVAL LNGTFYECAM SGTRSSGLLE LICKGKPKEC WEELHKVSCG K TSMLPTVN EELKLSLQAQ SQILGWCLIC SASFFSLLTT CYARCRSKVS YLQLSFWKTY AQKEKEQLEN TFLDYANKLS ER NLKCFFE NKRPDPFPMP TFAAWEAASE LHSFHQSQQH YSTLHRVVDN G

UniProtKB: Calcium homeostasis modulator protein 5

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Macromolecule #2: 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 2 / Number of copies: 55 / Formula: PA8
Molecular weightTheoretical: 423.458 Da
Chemical component information

ChemComp-PA8:
1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE

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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

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1099624
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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