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- PDB-6bbp: Model for compact volume of truncated monomeric Cytohesin-3 (Grp1... -

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Database: PDB / ID: 6bbp
TitleModel for compact volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
ComponentsCytohesin-3,ADP-ribosylation factor 6
KeywordsLIPID BINDING PROTEIN / Guanine nucleotide exchange factor / Arf GTPase / Fusion protein / Inositol 1 / 3 / 4 / 5-tetrakisphosphate
Specimen sourceMus musculus / mammal / House mouse /
Homo sapiens / human /
MethodElectron microscopy (35 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsDas, S. / Malaby, A.W. / Lambright, D.G.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2017 / Release: Jan 10, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 10, 2018Structure modelrepositoryInitial release
1.1Jan 17, 2018Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Deposited unit
A: Cytohesin-3,ADP-ribosylation factor 6
hetero molecules

Theoretical massNumber of molelcules
Total (without water)61,3404

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide Cytohesin-3,ADP-ribosylation factor 6 / ARF nucleotide-binding site opener 3 / Protein ARNO3 / General receptor of phosphoinositides 1 / Grp1 / PH / SEC7 and coiled-coil domain-containing protein 3 / CLM3 / SEC7 homolog C / mSec7-3

Mass: 60292.777 Da / Num. of mol.: 1 / Mutation: E161A,E161A
Source: (gene. exp.) Mus musculus / mammal / House mouse / , (gene. exp.) Homo sapiens / human /
Gene: Cyth3, Grp1, Pscd3, ARF6 / Production host: Escherichia coli / References: UniProt: O08967, UniProt: P62330

Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3 / : Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#3: Chemical ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / : Magnesium
#4: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE

Mass: 500.075 Da / Num. of mol.: 1 / Formula: C6H16O18P4

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein complex with GTP, Mg and Inositol 1,3,4,5 tetrakisphosphate
Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, and 0.001 mM IP4
pH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Details: Stained with 0.75% (w/v) uranyl formate / Material: Uranyl Formate
Specimen supportGrid material: COPPER / Grid mesh size: 400

Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI 12
Details: Gatan Erlang Shen 785 camera used for collecting images
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 / Nominal defocus max: 3200 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2
Details: Gatan Erlang Shen 785 camera used for collecting images
Film or detector model: OTHER / Number of grids imaged: 1 / Number of real images: 369


EM software
Image processingDetails: The images were X-ray corrected
Particle selectionDetails: EMAN2 based manual particle picking / Number of particles selected: 10000
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 6504 / Number of class averages: 71 / Symmetry type: POINT
Least-squares processHighest resolution: 35 Å

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