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- PDB-6bbq: Model for extended volume of truncated monomeric Cytohesin-3 (Grp... -

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Basic information

Entry
Database: PDB / ID: 6bbq
TitleModel for extended volume of truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein
DescriptorCytohesin-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 / Mouse / ハツカネズミ, はつかねずみ /
Homo sapiens / human
MethodElectron microscopy (35 Å resolution / Particle / Single particle)
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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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3554
Polyers60,3081
Non-polymers1,0483
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Polypeptide(L)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: 60307.855 Da / Num. of mol.: 1 / Mutation: E161A,E161A
Source: (gene. exp.) Mus musculus / mammal / ハツカネズミ, はつかねずみ / , (gene. exp.) Homo sapiens / human
References: UniProt: O08967, UniProt: P62330
#2: ChemicalChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP *YM


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3
#3: ChemicalChemComp-MG / MAGNESIUM ION


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


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A 6GS Arf6 Q67L fusion protein
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

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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

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Processing

EM software
IDNameVersionCategoryImage processing ID
4EMAN2CTF CORRECTION1
12EMAN2CLASSIFICATION1
13EMAN2RECONSTRUCTION1
Image processingDetails: The images were X-ray corrected
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: EMAN2 based manual particle picking / Number of particles selected: 10000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 6504 / Number of class averages: 71 / Symmetry type: POINT

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