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- EMDB-65251: alpha-dystroglycan structure using negative staining -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65251
Titlealpha-dystroglycan structure using negative staining
Map data
Sample
  • Tissue: alpha-dystroglycan
    • Protein or peptide: alpha-dystroglycan
Keywordsbinding protein / dumbbel shaped / glycoprotein / CARBOHYDRATE
Function / homology
Function and homology information


muscle attachment / dystroglycan complex / contractile ring / microtubule anchoring / nerve development / basement membrane organization / vinculin binding / structural constituent of muscle / alpha-actinin binding / membrane protein ectodomain proteolysis ...muscle attachment / dystroglycan complex / contractile ring / microtubule anchoring / nerve development / basement membrane organization / vinculin binding / structural constituent of muscle / alpha-actinin binding / membrane protein ectodomain proteolysis / basement membrane / negative regulation of MAPK cascade / laminin binding / tubulin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / SH2 domain binding / axon guidance / negative regulation of cell migration / morphogenesis of an epithelium / filopodium / sarcolemma / lamellipodium / actin binding / virus receptor activity / postsynaptic membrane / cytoskeleton / focal adhesion / calcium ion binding / extracellular space / nucleoplasm / cytoplasm
Similarity search - Function
Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan (Dystrophin-associated glycoprotein 1) / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Cadherin-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / negative staining / Resolution: 6.02 Å
AuthorsKasahata N
Funding support Japan, 1 items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Applied Cell Biology / Year: 2025
Title: Elucidating the Three-Dimensional Structure of alpha-dystroglycan using Negative Staining
Authors: Kasahata N
History
DepositionJul 3, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65251.png

Downloads & links

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Map

FileDownload / File: emd_65251.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 350 pix.
= 325.5 Å		0.93 Å/pix.
x 350 pix.
= 325.5 Å		0.93 Å/pix.
x 350 pix.
= 325.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.291
Minimum - Maximum-0.21733828 - 0.5343752
Average (Standard dev.)0.0015997614 (±0.031535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 325.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65251_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_65251_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 : alpha-dystroglycan

EntireName: alpha-dystroglycan
Components
  • Tissue: alpha-dystroglycan
    • Protein or peptide: alpha-dystroglycan

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Supramolecule #1: alpha-dystroglycan

SupramoleculeName: alpha-dystroglycan / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gallus gallus (chicken) / Organ: muscle / Tissue: muslce

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Macromolecule #1: alpha-dystroglycan

MacromoleculeName: alpha-dystroglycan / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken) / Strain: Broiler / Organ: MUSCLE / Tissue: muscle
SequenceString: MTVGCVPQPP FLGRTLLPVL LLAASARCHW PSEPAEVVRD WENQLEASMH SVLSDLRETV PAVVGIPDSS AVVGRFFRVS IPTDLIASNG EAVQVSEAGK ESLPSWLHWN AESSSLEGLP LDTDKGVHYI SVTTLQPFPN GSYVPQAANV FSVEVHQEDH SEPQSLRAAA ...String:
MTVGCVPQPP FLGRTLLPVL LLAASARCHW PSEPAEVVRD WENQLEASMH SVLSDLRETV PAVVGIPDSS AVVGRFFRVS IPTDLIASNG EAVQVSEAGK ESLPSWLHWN AESSSLEGLP LDTDKGVHYI SVTTLQPFPN GSYVPQAANV FSVEVHQEDH SEPQSLRAAA QEAGDAAPFV CGAEEPVTIL TVILDADLTK MTPKQRIELL NRMRSFSEVE LHNMKLVPVV NNRLFDMSAF MAGPGNAKKV VENGALLSWK LGCSLSQNSV PNISKVEAPA KEGTMSARLG YPVVGWHIAN KKPHLPKRMR RQINATPTPL TAIGPPTTAA QEPPTRIVPT PTSPAIAPPT ETTAPPVREP IPLPRKPTVT IRTRGPIVQT PTLGPIQPTR LVEGTGTVSV PIRPTVPGYV EPTAVITPPT TTTKKPRVST LKPATPSTTD SSTATTRRPT RRPKTPRPTK PPSTTRSTIS KLTTASPPTR VRTTASGVPR PWEPNEPPKL TNHIDRVDAW EGTYFEVKIP SDTFYDKEDT TTDKLQLTLK LKEQQMIEEN SWVQFNSTSQ LMYGMPDRSH VGKHEYFMYA TDKGGLFAVD AFEIHVHKRP HGDKSPVKFK ARLEGDHSAV ANDIHKKIML VKKLALAFGD RNSSTITVQD IAKGSIVVEW TNNTLPLEPC PREQIRTLSK KIADDSGGPS PAFSNILQPE FKPLNVSVVG SGSCRHIQFV PVTKDGRVIS EATPTLAAGK DPEKSSEDDV YLHTVIPAVV VAAILLVAGI IAMICYRKKR KGKLTIEDQA TFIKKGVPII FADELDDSKP PPSSSMPLIL QEEKAPLPPP EYPNQSMPET TPLNQDTIGE YTPLRDEDPN APPYQPPPPF TAPMEGKGSR PKNMTPYRSP PPYVPP

UniProtKB: Dystroglycan 1

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Details: 50 mM Tris-HCl 200 mM NaCl 0.2 mM PMSF 0.1 mM EDTA 125 microM protease inhibitor cocktail
StainingType: NEGATIVE / Material: uranyl acetate / Details: 2% uranyl acetate
GridModel: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 6mA

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Electron microscopy

MicroscopeJEOL 1230
Image recordingFilm or detector model: GATAN ORIUS SC200 (2k x 2k) / Number real images: 50 / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL

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Image processing

Particle selectionNumber selected: 7703
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: NONE
Startup modelType of model: OTHER / Details: ab-initio
Final reconstructionNumber classes used: 6 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1)
Details: The resolution estimated FSC curve was 6.02. However, since this study is based on negative staining data, true resolusion seemed to be lower.
Number images used: 596
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final 3D classificationNumber classes: 50 / Avg.num./class: 140 / Software - Name: cryoSPARC (ver. 4.3.1)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL / Overall B value: 143.2

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