3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-8900

This page is a legacy version and will be discarded in future. The new page is here.

Negative stain reconstruction of human autophagy associated protein, ATG2A

by single particle reconstruction, at 29.4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 5.2, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 5.2, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 8900
TitleNegative stain reconstruction of human autophagy associated protein, ATG2A
MapNegative stain reconstruction of human ATG2A protein
SampleHuman ATG2A protein
AuthorsChowdhury S, Otomo C, Leitner A, Ohashi K, Aebersold R, Lander GC, Otomo T
DateDeposition: 2017-08-21, Header release: 2017-09-06, Map release: 2017-09-06, Last update: 2017-09-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 5.2, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 5.2, Imaged by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - Primary
ArticleTo be published
TitleTo Be Published
AuthorsChowdhury S, Otomo C, Leitner A, Ohashi K, Aebersold R, Lander GC, Otomo T
Map
Fileemd_8900.map.gz ( map file in CCP4 format, 3539 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
4.1 A/pix
= 393.6 A
96 pix
4.1 A/pix
= 393.6 A
96 pix
4.1 A/pix
= 393.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:5.2 (by author), 5.2 (movie #1):
Minimum - Maximum: -5.7097316 - 19.625645
Average (Standard dev.): 0.057370227 (0.7065861)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin000
Limit959595
Spacing969696
Unit CellA= B= C: 393.59998 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.1 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.14.14.1
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z393.600393.600393.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.71019.6260.057
Annotation DetailsNegative stain reconstruction of human ATG2A protein
Supplement
Images
Images
Sample
NameHuman ATG2A protein
Number of Components1
Theoretical Mass0.2MDa
DetailsFull length protein
Component #1: protein - Human ATG2A protein
Scientific nameHuman ATG2A protein
Theoretical Mass0.2 MDa
DetailsFull length protein
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 7108
Expression system: Spodoptera frugiperda
Exp System Strain: 9
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.01 mg/ml
BufferpH: 7.5
Vitrification
Cryogen NameNONE
Imaging
MicroscopeFEI TECNAI SPIRIT
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 52000, Calibrated: 52000
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 1500 nm
Specimen Holder
ModelSIDE ENTRY, EUCENTRIC
Temperature K ( 273.15 - 298.15 K)
Camera
DetectorTVIPS TEMCAM-F416 (4k x 4k)
Image Acquisition
#1
Number of Digital Images590
Sampling Size15.6
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRelion
Resolution By Author29.4 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections6386
Download
Data from EMDB
Header (meta data in XML format)emd-8900-v19.xml (5.9 KB)
emd-8900-v20.xml (13.1 KB)
emd-8900.xml (5.9 KB)
Map dataemd_8900.map.gz (249.7 KB)
Imagesemd_8900.png (26.4 KB)
Othersemd_8900_additional.map.gz (2.4 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-8900
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.4 KB