6U3E | pdb_00006u3e

Best fitting antiparallel model for Volume 1 of truncated dimeric Cytohesin-3 (Grp1; amino acids 14-399)

• PDB DOI: https://doi.org/10.2210/pdb6U3E/pdb
• EM Map EMD-20628: EMDB EMDataResource

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-08-21 Released: 2019-09-25 
• Deposition Author(s): Das, S., Lambright, D.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 53.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.

Das, S., Malaby, A.W., Nawrotek, A., Zhang, W., Zeghouf, M., Maslen, S., Skehel, M., Chakravarthy, S., Irving, T.C., Bilsel, O., Cherfils, J., Lambright, D.G.

(2019) Structure 27: 1782

• PubMed: 31601460 
• DOI: https://doi.org/10.1016/j.str.2019.09.007
• Primary Citation Related Structures: 
  6U3E, 6U3G


• PubMed Abstract: 
  

  Membrane dynamic processes require Arf GTPase activation by guanine nucleotide exchange factors (GEFs) with a Sec7 domain. Cytohesin family Arf GEFs function in signaling and cell migration through Arf GTPase activation on the plasma membrane and endosomes. In this study, the structural organization of two cytohesins (Grp1 and ARNO) was investigated in solution by size exclusion-small angle X-ray scattering and negative stain-electron microscopy and on membranes by dynamic light scattering, hydrogen-deuterium exchange-mass spectrometry and guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange assays. The results suggest that cytohesins form elongated dimers with a central coiled coil and membrane-binding pleckstrin-homology (PH) domains at opposite ends. The dimers display significant conformational heterogeneity, with a preference for compact to intermediate conformations. Phosphoinositide-dependent membrane recruitment is mediated by one PH domain at a time and alters the conformational dynamics to prime allosteric activation by Arf-GTP. A structural model for membrane targeting and allosteric activation of full-length cytohesin dimers is discussed.

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Organizational Affiliation: 
• Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
CNRS and Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France.
MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA.
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
CNRS and Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France. Electronic address: [e-mail].
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, equilibrium centrifugation, gel filtration

Macromolecule Content 

• Total Structure Weight: 94 kDa 
• Atom Count: 6,594 
• Modeled Residue Count: 794 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytohesin-3	A, B	397	Homo sapiens	Mutation(s): 0  Gene Names: CYTH3, ARNO3, GRP1, PSCD3
UniProt & NIH Common Fund Data Resources
Find proteins for O43739 (Homo sapiens) Explore O43739  Go to UniProtKB:  O43739
PHAROS:  O43739 GTEx:  ENSG00000008256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IP	C [auth A], D [auth B]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4IP	BindingDB:  6U3E	Kd: 100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 53.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN2	2.12

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Das, S., Lambright, D.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM056324

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-10-23
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Database references
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description