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- PDB-1joc: EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-di... -

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Basic information

Entry
Database: PDB / ID: 1joc
TitleEEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate
ComponentsEarly Endosomal Autoantigen 1
KeywordsMEMBRANE PROTEIN / FYVE domain / inositol 3-phosphate binding
Function / homology
Function and homology information


synaptic vesicle to endosome fusion / postsynaptic early endosome / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / axonal spine / chemical synaptic transmission, postsynaptic / presynaptic endosome / host-mediated perturbation of viral process / early endosome to late endosome transport / GTP-dependent protein binding ...synaptic vesicle to endosome fusion / postsynaptic early endosome / Toll Like Receptor 9 (TLR9) Cascade / 1-phosphatidylinositol binding / axonal spine / chemical synaptic transmission, postsynaptic / presynaptic endosome / host-mediated perturbation of viral process / early endosome to late endosome transport / GTP-dependent protein binding / vesicle fusion / recycling endosome / Schaffer collateral - CA1 synapse / endocytosis / early endosome membrane / early endosome / calmodulin binding / glutamatergic synapse / protein homodimerization activity / extracellular exosome / zinc ion binding / cytosol
Similarity search - Function
L1 transposable element, trimerization domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. ...L1 transposable element, trimerization domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger C2H2-type / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ITP / Early endosome antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsDumas, J.J. / Merithew, E. / Rajamani, D. / Hayes, S. / Lawe, D. / Corvera, S. / Lambright, D.G.
CitationJournal: Mol.Cell / Year: 2001
Title: Multivalent endosome targeting by homodimeric EEA1.
Authors: Dumas, J.J. / Merithew, E. / Sudharshan, E. / Rajamani, D. / Hayes, S. / Lawe, D. / Corvera, S. / Lambright, D.G.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Early Endosomal Autoantigen 1
B: Early Endosomal Autoantigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2208
Polymers28,2782
Non-polymers9426
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-31 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.528, 85.096, 88.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Early Endosomal Autoantigen 1 / EEA1


Mass: 14139.077 Da / Num. of mol.: 2 / Fragment: C-terminal domain, FYVE domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15075
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ITP / PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER / INOSITOL 1,3-BISPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 11% PEG 4000, 50 mM HEPES, 60 mM ammonium acetate, 10% glycerol, and 1.5 mM Ins(1,3)P2, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
211 %PEG40001reservoir
350 mMHEPES1reservoirpH7.0
460 mMammonium acetate1reservoir
51.5 mMIns(1,3)P21reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.28322, 1.28356, 1.23985
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Mar 20, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.283221
21.283561
31.239851

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.221 / Stereochemistry target values: Engh & Huber
Details: Residues 1287 and 1288 were missing from the electron density.
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 44 56 2038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.1

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