[English] 日本語
Yorodumi
- PDB-6bbp: Model for compact volume of truncated monomeric Cytohesin-3 (Grp1... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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
Function / homologyP-loop containing nucleoside triphosphate hydrolase / small GTPase Arf family profile. / PH domain / Sec7 domain superfamily / Sec7 domain / Sec7 domain / Pleckstrin homology domain / Small GTP-binding protein domain / PH domain profile. / ADP-ribosylation factor family ...P-loop containing nucleoside triphosphate hydrolase / small GTPase Arf family profile. / PH domain / Sec7 domain superfamily / Sec7 domain / Sec7 domain / Pleckstrin homology domain / Small GTP-binding protein domain / PH domain profile. / ADP-ribosylation factor family / SEC7 domain profile. / Small GTPase superfamily, ARF/SAR type / PH-like domain superfamily / TBC/RABGAPs / Clathrin-mediated endocytosis / MET receptor recycling / Sec7, C-terminal domain superfamily / in:ipr024156: / myeloid cell apoptotic process / protein localization to endosome / regulation of dendritic spine development / regulation of ARF protein signal transduction / Golgi vesicle transport / establishment of epithelial cell polarity / negative regulation of receptor-mediated endocytosis / ruffle assembly / regulation of Rac protein signal transduction / endocytic recycling / negative regulation of protein localization to cell surface / negative regulation of dendrite development / ARF guanyl-nucleotide exchange factor activity / regulation of filopodium assembly / Flemming body / thioesterase binding / protein localization to cell surface / filopodium membrane / cortical actin cytoskeleton organization / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / hepatocyte apoptotic process / positive regulation of cell adhesion / positive regulation of actin filament polymerization / adherens junction / bicellular tight junction / guanyl-nucleotide exchange factor activity / vesicle-mediated transport / endocytic vesicle / ruffle / liver development / positive regulation of protein localization to plasma membrane / recycling endosome membrane / cell cortex / protein transport / extrinsic component of cytoplasmic side of plasma membrane / protein N-terminus binding / early endosome / endosome / GTPase activity / cell cycle / cell adhesion / cell division / myelin sheath / GTP binding / focal adhesion / Golgi apparatus / membrane / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm / Cytohesin-3 / ADP-ribosylation factor 6
Function and homology information
Specimen sourceMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / 35 Å resolution
AuthorsDas, S. / Malaby, A.W. / Lambright, D.G.
CitationJournal: Structure / Year: 2018
Title: Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors.
Authors: Andrew W Malaby / Sanchaita Das / Srinivas Chakravarthy / Thomas C Irving / Osman Bilsel / David G Lambright
Abstract: Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and ...Membrane dynamic processes including vesicle biogenesis depend on Arf guanosine triphosphatase (GTPase) activation by guanine nucleotide exchange factors (GEFs) containing a catalytic Sec7 domain and a membrane-targeting module such as a pleckstrin homology (PH) domain. The catalytic output of cytohesin family Arf GEFs is controlled by autoinhibitory interactions that impede accessibility of the exchange site in the Sec7 domain. These restraints can be relieved through activator Arf-GTP binding to an allosteric site comprising the PH domain and proximal autoinhibitory elements (Sec7-PH linker and C-terminal helix). Small-angle X-ray scattering and negative-stain electron microscopy were used to investigate the structural organization and conformational dynamics of cytohesin-3 (Grp1) in autoinhibited and active states. The results support a model in which hinge dynamics in the autoinhibited state expose the activator site for Arf-GTP binding, while subsequent C-terminal helix unlatching and repositioning unleash conformational entropy in the Sec7-PH linker to drive exposure of the exchange site.
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7077
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,3404
Polyers60,2931
Non-polymers1,0483
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#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 (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Cyth3, Grp1, Pscd3, ARF6 / Production host: Escherichia coli (E. coli) / References: UniProt: O08967, UniProt: P62330
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
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 (house mouse)
Source (recombinant)Organism: Escherichia coli (E. 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 FIELDBright-field microscopy / 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

-
Processing

EM software
IDNameVersionCategory
4EMAN2CTF correction
12EMAN2classification
13EMAN23D reconstruction
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
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more