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- EMDB-62246: Cryo-EM structure of docked mouse bestrophin-1 in a partial open state -

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Basic information

Entry
Database: EMDB / ID: EMD-62246
TitleCryo-EM structure of docked mouse bestrophin-1 in a partial open state
Map data
Sample
  • Complex: Docked Pentameric structure of mouse bestrophin-1 in a partial open state
    • Protein or peptide: Bestrophin-1,Soluble cytochrome b562
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION
KeywordsDocked / Partial open / Calcium-bound / Membrane protein
Function / homology
Function and homology information


membrane microdomain / bicarbonate channel activity / gamma-aminobutyric acid secretion, neurotransmission / transepithelial chloride transport / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / detection of light stimulus involved in visual perception / Stimuli-sensing channels / glutamate secretion / chloride transport ...membrane microdomain / bicarbonate channel activity / gamma-aminobutyric acid secretion, neurotransmission / transepithelial chloride transport / ligand-gated channel activity / intracellularly calcium-gated chloride channel activity / detection of light stimulus involved in visual perception / Stimuli-sensing channels / glutamate secretion / chloride transport / chloride channel activity / protein complex oligomerization / regulation of calcium ion transport / chloride channel complex / electron transport chain / regulation of synaptic plasticity / presynapse / basolateral plasma membrane / periplasmic space / electron transfer activity / iron ion binding / heme binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Bestrophin / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Bestrophin-1 / Soluble cytochrome b562
Similarity search - Component
Biological speciesMus musculus (house mouse) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLim HH / Kim KW / Ko A
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
National Research Foundation (NRF, Korea)2020 M3E5D9079 to H.-H.L. Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionNov 1, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62246.png

Downloads & links

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Map

FileDownload / File: emd_62246.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.9699717 - 8.376099
Average (Standard dev.)0.00021609584 (±0.24568275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62246_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_62246_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 : Docked Pentameric structure of mouse bestrophin-1 in a partial op...

EntireName: Docked Pentameric structure of mouse bestrophin-1 in a partial open state
Components
  • Complex: Docked Pentameric structure of mouse bestrophin-1 in a partial open state
    • Protein or peptide: Bestrophin-1,Soluble cytochrome b562
  • Ligand: CALCIUM ION
  • Ligand: CHLORIDE ION

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Supramolecule #1: Docked Pentameric structure of mouse bestrophin-1 in a partial op...

SupramoleculeName: Docked Pentameric structure of mouse bestrophin-1 in a partial open state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Bestrophin-1,Soluble cytochrome b562

MacromoleculeName: Bestrophin-1,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 79.285266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTITYTNKVA NARLGSFSSL LLCWRGSIYK LLYGEFLVFI FLYYSIRGLY RMVLSSDQQL LFEKLALYCD SYIQLIPISF VLGFYVTLV VSRWWSQYEN LPWPDRLMIQ VSSFVEGKDE EGRLLRRTLI RYAILGQVLI LRSISTSVYK RFPTLHHLVL A GFMTHGEH ...String:
MTITYTNKVA NARLGSFSSL LLCWRGSIYK LLYGEFLVFI FLYYSIRGLY RMVLSSDQQL LFEKLALYCD SYIQLIPISF VLGFYVTLV VSRWWSQYEN LPWPDRLMIQ VSSFVEGKDE EGRLLRRTLI RYAILGQVLI LRSISTSVYK RFPTLHHLVL A GFMTHGEH KQLQKLGLPH NTFWVPWVWF ANLSMKAYLG GRIRDTVLLQ SLMNEVCTLR TQCGQLYAYD WISIPLVYTQ VV TVAVYSF FLACLIGRQF LNPNKDYPGH EMDLVVPVFT ILQFLFYMGW LKVAEQLINP FGEDDDDFET NWIIDRNLQV SLL SVDGMH QNLPPMERDM YWNEAAPQPP YTAASARSRR HSFMGSTFNI SLKKEDLELW SKEEADTDKK ESGYSSTIGC FLGL QPKNY HLPLKDLKTK LLCSKNPLLE GQCKDANQKN QKDVWKFKGL DFLKCVPRFK RRGSHCGPQA PSSHPTEQSA PSSSD TGDG PSTDYQEICH MKKKTVEFNL NIPESPTEHL QQRRLDQMST NIQALMKEHA ESYPYRDEAG TKPVLYETGL EVLFQG PAD LEDNWETLND NLKVIEKADN AAQVKDALTK MRAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLA NE GKVKEAQAAA EQLKTTRNAY IQKYLDYKDH DGDYKDHDID YKDDDDK

UniProtKB: Bestrophin-1, Soluble cytochrome b562

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97720
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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