Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.22 kDa 
• Atom Count: 2025 
• Residue Count: 246 
• Unique protein chains: 1

1JOC

EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate

• DOI: 10.2210/pdb1JOC/pdb

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


• Deposited: 2001-07-27 Released: 2001-12-28 
• Deposition Author(s): Dumas, J.J., Merithew, E., Rajamani, D., Hayes, S., Lawe, D., Corvera, S., Lambright, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 

Literature

Multivalent endosome targeting by homodimeric EEA1.

Dumas, J.J., Merithew, E., Sudharshan, E., Rajamani, D., Hayes, S., Lawe, D., Corvera, S., Lambright, D.G.

(2001) Mol Cell 8: 947-958

• PubMed: 11741531 
• DOI: 10.1016/s1097-2765(01)00385-9
• Primary Citation of Related Structures:  
  1JOC


• PubMed Abstract: 
  

Early endosome autoantigen localization to early endosomes is mediated by a C-terminal region, which includes a calmodulin binding motif, a Rab5 interaction site, and a FYVE domain that selectively binds phosphatidyl inositol 3-phosphate. The crystal structure of the C-terminal region bound to inositol 1,3-bisphosphate reveals an organized, quaternary assembly consisting of a parallel coiled coil and a dyad-symmetric FYVE domain homodimer. Structural and biochemical observations support a multivalent mechanism for endosomal localization in which domain organization, dimerization, and quaternary structure amplify the weak affinity and modest specificity of head group interactions with conserved residues. A unique mode of membrane engagement deduced from the quaternary structure of the C-terminal region provides insight into the structural basis of endosome tethering.

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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
Early Endosomal Autoantigen 1	A, B	125	Homo sapiens	Mutation(s): 0  Gene Names: EEA1, ZFYVE2
Find proteins for Q15075 (Homo sapiens) Explore Q15075  Go to UniProtKB:  Q15075
NIH Common Fund Data Resources
PHAROS:  Q15075 GTEx:  ENSG00000102189

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ITP	A, B	PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER C6 H14 O12 P2 PUVHMWJJTITUGO-FICORBCRSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ITP	Kd:  24000   nM  Binding MOAD
ITP	Kd :  24000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.528	α = 90
b = 85.096	β = 90
c = 88.036	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-27 
• Released Date: 2001-12-28 
Deposition Author(s): Dumas, J.J., Merithew, E., Rajamani, D., Hayes, S., Lawe, D., Corvera, S., Lambright, D.G.

Revision History 

• Version 1.0: 2001-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance