4KAX

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.USA 110: 14213-14218

  • DOI: 10.1073/pnas.1301883110

  • 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 me ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosylation factor 6
A
169Homo sapiensMutation(s): 1 
Gene Names: ARF6
Find proteins for P62330 (Homo sapiens)
Go to Gene View: ARF6
Go to UniProtKB:  P62330
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytohesin-3
B
161Homo sapiensMutation(s): 0 
Gene Names: CYTH3 (ARNO3, GRP1, PSCD3)
Find proteins for O43739 (Homo sapiens)
Go to Gene View: CYTH3
Go to UniProtKB:  O43739
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GTP
Query on GTP

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A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
4IP
Query on 4IP

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B
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
C6 H16 O18 P4
CIPFCGZLFXVXBG-CNWJWELYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4IPKd: 100 nM (99) BINDINGDB
GTPKd: 17000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.595α = 90.00
b = 56.595β = 90.00
c = 274.371γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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