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- EMDB-7639: Single-Molecule 3D Image of neurexin 1 alpha by Individual Partic... -

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Basic information

Entry
Database: EMDB / ID: EMD-7639
TitleSingle-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 001)
Map dataneurexin 1 alpha
Sample
  • Organelle or cellular component: neurexin 1 alpha
Biological speciesBos taurus (domestic cattle)
Methodelectron tomography / negative staining / Resolution: 15.08 Å
AuthorsLiu JF / Misra A / Reddy S / White MA / Ren G / Rudenko G
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Plasticity of Neurexin 1 alpha : Implications for its Role as Synaptic Organizer.
Authors: Liu J / Misra A / Reddy MVVVS / White MA / Ren G / Rudenko G
History
DepositionMar 27, 2018-
Header (metadata) releaseMay 16, 2018-
Map releaseSep 19, 2018-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_7639.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationneurexin 1 alpha
Voxel sizeX=Y=Z: 1.48 Å
Density
Contour LevelMovie #1: 0.5
Minimum - Maximum-0.24938476 - 5.002565
Average (Standard dev.)0.02516621 (±0.16050805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.481.481.48
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z331.520331.520331.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-0.2495.0030.025

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Supplemental data

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Sample components

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Entire : neurexin 1 alpha

EntireName: neurexin 1 alpha
Components
  • Organelle or cellular component: neurexin 1 alpha

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Supramolecule #1: neurexin 1 alpha

SupramoleculeName: neurexin 1 alpha / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 137 KDa
Recombinant expressionOrganism: unidentified baculovirus

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 25 mM Tris pH 8, 100 mM NaCl, 3 mM CaCl2
StainingType: NEGATIVE / Material: uranyl formate
Details: The grid was stained for 15 s by sequential submersion in two drops of uranyl formate (UF).
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
DetailsThe purified neurexin 1 alpha proteins were stored in 25 mM Tris pH 8, 100 mM NaCl in flash-frozen aliquots.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 81 / Average exposure time: 1.0 sec. / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 80000

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Image processing

DetailsX-ray speckles in images were removed before alignment and 3D reconstruction.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.08 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The 3D reconstruction was performed by Individual-Particle Electron Tomography (IPET).
Number images used: 65
CTF correctionSoftware: (Name: TOMOCTF, IMOD)
Details: Micrographs were aligned together by IMOD. The CTF was corrected by TOMOCTF.

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