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1hyi

SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN COMPLEXED WITH INOSITOL 1,3-BISPHOSPHATE

Method: SOLUTION NMR Dmax: 40.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ENDOSOME-ASSOCIATED PROTEIN

Homo sapiens

UniProt Q15075

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1346–1410 Fragment：FYVE DOMAIN (RESIDUES 1346-1410) ZN ZINC ION × 2 ITP PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER × 1 SOLUTION NMR NMR measurement conditions：pH 6.7；298 K；Ionic strength (raw mmCIF value) 200 mM KCl；Pressure 1 NMR sample composition：1mM FYVE domain; 20 mM d-Tris buffer; pH 6.7; 200 mM KCl; 20 mM d-DTT; 1 mM NaN3 | 90% H2O/10% D2O NMR sample composition：1mM FYVE domain; 20 mM d-Tris buffer; pH 6.7; 200 mM KCl; 20 mM d-DTT; 1 mM NaN3 | 99.99% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1HYI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HYJ SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN Deposited 2001-01-19 Different ligand/ion Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1346–1410（65 aa） Fragment：FYVE DOMAIN (RESIDUES 1346-1410)
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 200 mM KCl；Pressure 1
NMR sample composition 1mM FYVE domain; 20 mM d-Tris buffer; pH 6.7; 200 mM KCl; 20 mM d-DTT; 1 mM NaN3 | 90% H2O/10% D2O
NMR sample composition 1mM FYVE domain; 20 mM d-Tris buffer; pH 6.7; 200 mM KCl; 20 mM d-DTT; 1 mM NaN3 | 99.99% D2O
Resolution not provided
1JOC EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate Deposited 2001-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1287–1410（124 aa） Fragment：C-terminal domain, FYVE domain
Chain B 1287–1410（124 aa） Fragment：C-terminal domain, FYVE domain
Not recorded ZN ZINC ION × 4 ITP PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；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
Resolution 2.20 Å R-free 0.281
3MJH Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 Deposited 2010-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 36–69（34 aa） Fragment：C2H2-type, residues 36-69
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.03 Å R-free 0.260
3MJH Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 Deposited 2010-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 36–69（34 aa） Fragment：C2H2-type, residues 36-69
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG 4000, 50mM sodium acetate, 0.2M sodium-potassium phosphate, 10% glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.03 Å R-free 0.260

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EEA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–65； UniProt 1346–1410

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1hyi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1hyi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1hyi
Deposition date deposition_date2001-01-19
Structure title titleSOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN COMPLEXED WITH INOSITOL 1,3-BISPHOSPHATE
Keywords keywordsbeta sheet, alpha helix, zinc cluster, PtdIns(3)P, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.47 Å
Radius of gyration Rg (electron density) rg_electron11.88 Å
Forward intensity I(0) i0465745000.00
Molecular weight molecular_weight153900.0 kDa
Excluded volume excluded_volume180970 ų
Envelope volume envelope_volume17413 ų
Hydration-shell volume shell_volume10979 ų
Envelope diameter envelope_diameter44.9 Å
Shell Rg shell_rg19.31 Å
Envelope Rg envelope_rg14.27 Å
Shape Rg shape_rg11.92 Å
Total Rg total_rg11.89 Å
Total atoms total_atoms20300
Residues n_residues1300
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax40.9 Å
Rg (real space) rg_real11.48 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real4.6570e+08
I(0) uncertainty (real space) i0_real_error4.8670e+06
Rg (reciprocal space) rg_reciprocal11.48 Å
I(0) (reciprocal space) i0_reciprocal465700000.0000
Solution quality estimate total_estimate0.8310
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary13.4 Å
Skewness Skewness skewness0.376
Kurtosis Kurtosis kurtosis-0.196
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha149600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.621; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.995
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1hyia_
Class classg — Small proteins
Fold Fold foldg.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamilyg.50.1 — FYVE/PHD zinc finger
Family Family familyg.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

CATH v4.4 (1 domains)

Domain ID domain_id1hyiA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
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8. Citations (1)

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9. Files and Curves (10)