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- EMDB-3712: Human BBsome core complex with subunits BBS1, BBS4, BBS5, BBS8, B... -

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Basic information

Entry
Database: EMDB / ID: 3712
TitleHuman BBsome core complex with subunits BBS1, BBS4, BBS5, BBS8, BBS9, BBS18
Map dataNegative Stain Reconstruction:BBsome Complex
SampleA 6subunit, BBsome complex.:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 23 Å resolution
AuthorsKlink BU / Zent E / Juneja P / Kuhlee A / Raunser S / Wittinghofer A
CitationJournal: Elife / Year: 2017
Title: A recombinant BBSome core complex and how it interacts with ciliary cargo.
Authors: Björn Udo Klink / Eldar Zent / Puneet Juneja / Anne Kuhlee / Stefan Raunser / Alfred Wittinghofer
DateDeposition: May 8, 2017 / Header (metadata) release: Jun 14, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3712.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.89 Å/pix.
= 340.2 Å
180 pix
1.89 Å/pix.
= 340.2 Å
180 pix
1.89 Å/pix.
= 340.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density
Contour Level:0.7 (by author), 0.7 (movie #1):
Minimum - Maximum0 - 7.2863293
Average (Standard dev.)0.022554556 (0.22782631)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 340.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z340.200340.200340.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean0.0007.2860.023

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Supplemental data

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Sample components

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Entire A 6subunit, BBsome complex.

EntireName: A 6subunit, BBsome complex.
Details: Subunits: BBsome subunit 1 BBsome subunit 4 BBsome subunit 5 BBsome subunit 8 BBsome subunit 9 BBsome subunit18
Number of components: 1
MassTheoretical: 330 kDa

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Component #1: protein, A 6subunit, BBsome complex.

ProteinName: A 6subunit, BBsome complex.
Details: Subunits: BBsome subunit 1 BBsome subunit 4 BBsome subunit 5 BBsome subunit 8 BBsome subunit 9 BBsome subunit18
Recombinant expression: No
MassTheoretical: 330 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper) / Cell of expression system: High Five cells

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionBuffer solution: 50 mM Hepes pH 8.0, 150 mM NaCl, 5 mM MgCl2, 10% glycerol and 1 mM TCEP
pH: 8
Support filmGlow discharged 400 mesh copper grids with thin carbon support.
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1400
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal) / Cs: 3.4 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 1800 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 197

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 8339
3D reconstructionSoftware: SPARX / Resolution: 23 Å / Resolution method: FSC 0.5 CUT-OFF

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