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- EMDB-7078: Model for extended volume of truncated monomeric Cytohesin-3 (Grp... -

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Basic information

Entry
Database: EMDB / ID: 7078
TitleModel for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein
SampleTruncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
SourceMus musculus / mammal / ハツカネズミ, はつかねずみ /
Map dataExtended volume for truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein,
Methodsingle particle reconstruction, at 35 Å resolution
AuthorsDas S / Malaby AW
CitationStructure, 2018, 26, 106-117.e6

Structure, 2018, 26, 106-117.e6 Yorodumi Papers
Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors.
Andrew W Malaby / Sanchaita Das / Srinivas Chakravarthy / Thomas C Irving / Osman Bilsel / David G Lambright

Validation ReportPDB-ID: 6bbq

SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2017 / Header (metadata) release: Jan 10, 2018 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0639
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0639
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6bbq
  • Surface level: 0.0639
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_7078.map.gz (map file in CCP4 format, 2049 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/pix.
= 280. Å
80 pix
3.5 Å/pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.5 Å
Density
Contour Level:0.0639 (by author), 0.0639 (movie #1):
Minimum - Maximum-0.81098795 - 2.976905
Average (Standard dev.)-0.0019418432 (0.15161914)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin-40-40-40
Limit393939
Spacing808080
CellA=B=C: 280 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-0.8112.977-0.002

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Supplemental data

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Sample components

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Entire Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A ...

EntireName: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
Number of components: 5

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Component #1: protein, Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-39...

ProteinName: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
Recombinant expression: No
SourceSpecies: Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Cytohesin-3,ADP-ribosylation factor 6

ProteinName: Cytohesin-3,ADP-ribosylation factor 6 / Recombinant expression: No
MassTheoretical: 60.307855 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #3: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #4: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #5: ligand, INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

LigandName: INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.500075 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
pH: 8
StainingStained with 0.75% (w/v) uranyl formate
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12
Details: Gatan Erlang Shen 785 camera used for collecting images
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 60000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3200 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 369
Details: Gatan Erlang Shen 785 camera used for collecting images

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 6504 / Details: The images were X-ray corrected
3D reconstructionSoftware: EMAN / Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF

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Atomic model buiding

Output model

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