Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.22 kDa 
• Atom Count: 3026 
• Modelled Residue Count: 306 
• Deposited Residue Count: 330 
• Unique protein chains: 2

4KAX

Crystal structure of the Grp1 PH domain in complex with Arf6-GTP

• DOI: 10.2210/pdb4KAX/pdb

• Classification: PROTEIN BINDING/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-23 Released: 2013-08-14 
• Deposition Author(s): Lambright, D.G., Malaby, A.W., van den Berg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors.

Malaby, A.W., van den Berg, B., Lambright, D.G.

(2013) Proc Natl Acad Sci U S A 110: 14213-14218

• PubMed: 23940353 
• DOI: 10.1073/pnas.1301883110
• Primary Citation of Related Structures:  
  4KAX


• PubMed Abstract: 
  

Membrane recruitment of cytohesin family Arf guanine nucleotide exchange factors depends on interactions with phosphoinositides and active Arf GTPases that, in turn, relieve autoinhibition of the catalytic Sec7 domain through an unknown structural mechanism. Here, we show that Arf6-GTP relieves autoinhibition by binding to an allosteric site that includes the autoinhibitory elements in addition to the PH domain. The crystal structure of a cytohesin-3 construct encompassing the allosteric site in complex with the head group of phosphatidyl inositol 3,4,5-trisphosphate and N-terminally truncated Arf6-GTP reveals a large conformational rearrangement, whereby autoinhibition can be relieved by competitive sequestration of the autoinhibitory elements in grooves at the Arf6/PH domain interface. Disposition of the known membrane targeting determinants on a common surface is compatible with multivalent membrane docking and subsequent activation of Arf substrates, suggesting a plausible model through which membrane recruitment and allosteric activation could be structurally integrated.

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Organizational Affiliation: 

Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor 6	A	169	Homo sapiens	Mutation(s): 1  Gene Names: ARF6
Find proteins for P62330 (Homo sapiens) Explore P62330  Go to UniProtKB:  P62330
NIH Common Fund Data Resources
PHAROS:  P62330 GTEx:  ENSG00000165527

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytohesin-3	B	161	Homo sapiens	Mutation(s): 0  Gene Names: CYTH3, ARNO3, GRP1, PSCD3
Find proteins for O43739 (Homo sapiens) Explore O43739  Go to UniProtKB:  O43739
NIH Common Fund Data Resources
PHAROS:  O43739 GTEx:  ENSG00000008256

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	A	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
4IP	B	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N
CIT	A	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GTP	Kd :  17000   nM  PDBBind
4IP	Kd:  100   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.595	α = 90
b = 56.595	β = 90
c = 274.371	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-23 
• Released Date: 2013-08-14 
Deposition Author(s): Lambright, D.G., Malaby, A.W., van den Berg, B.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 1.2: 2013-09-11
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description