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- EMDB-40907: Cryo-EM Structure of NINJ2 Filament at 3.07 Angstrom Resolution -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40907
TitleCryo-EM Structure of NINJ2 Filament at 3.07 Angstrom Resolution
Map dataCryo-EM Map of NINJ2 Filament
Sample
  • Organelle or cellular component: Ninjurin-2 in complex with Cholesterol
    • Protein or peptide: Ninjurin-2
  • Ligand: CHOLESTEROL
KeywordsNINJ2 Filament / NINJ1 Paralog Protein / Cholesterol Binding Protein / Lipid Binding Protein / MEMBRANE PROTEIN
Function / homologyNinjurin / Ninjurin / neuron cell-cell adhesion / tissue regeneration / nervous system development / cell adhesion / plasma membrane / Ninjurin-2
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsSahoo B / Dai X
Funding support United States, 1 items
OrganizationGrant numberCountry
Other privateStartup Grant United States
CitationJournal: Biorxiv / Year: 2023
Title: How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot
Authors: Sahoo B / Mou Z / Liu W / Dubyak G / Dai X
History
DepositionMay 29, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40907.png

Downloads & links

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Map

FileDownload / File: emd_40907.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM Map of NINJ2 Filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å		0.66 Å/pix.
x 360 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.78082556 - 1.3811183
Average (Standard dev.)0.0024662488 (±0.03820898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM Half Map A of NINJ2 Filament

Fileemd_40907_half_map_1.map
AnnotationCryo-EM Half Map A of NINJ2 Filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM Half Map B of NINJ2 Filament

Fileemd_40907_half_map_2.map
AnnotationCryo-EM Half Map B of NINJ2 Filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ninjurin-2 in complex with Cholesterol

EntireName: Ninjurin-2 in complex with Cholesterol
Components
  • Organelle or cellular component: Ninjurin-2 in complex with Cholesterol
    • Protein or peptide: Ninjurin-2
  • Ligand: CHOLESTEROL

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Supramolecule #1: Ninjurin-2 in complex with Cholesterol

SupramoleculeName: Ninjurin-2 in complex with Cholesterol / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ninjurin-2

MacromoleculeName: Ninjurin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.615115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDYKDHDGDY KDHDIDYKDD DDKGSGESAR ENIDLQPGSS DPRSQPINLN HYATKKSVAE SMLDVALFMS NAMRLKAVLE QGPSSHYYT TLVTLISLSL LLQVVIGVLL VVIARLNLNE VEKQWRLNQL NNAATILVFF TVVINVFITA FGAHKTGFLA A RASRNPL

UniProtKB: Ninjurin-2

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 375439
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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