SAXSdb — 1joc

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Early Endosomal Autoantigen 1

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1287–1410 Chain B； UniProt 1287–1410	Fragment：C-terminal domain, FYVE domain	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

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 1JOC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HYI SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN COMPLEXED WITH INOSITOL 1,3-BISPHOSPHATE Deposited 2001-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 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
1HYJ SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN Deposited 2001-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
3MJH Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1 Deposited 2010-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 1–125； UniProt 1287–1410 Author chain B； PDBConstruct 1–125； UniProt 1287–1410

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1joc
Deposition date deposition_date	2001-07-27
Structure title title	EEA1 homodimer of C-terminal FYVE domain bound to inositol 1,3-diphosphate
Keywords keywords	FYVE domain, inositol 3-phosphate binding, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.12 Å
Radius of gyration Rg (electron density) rg_electron	33.69 Å
Forward intensity I(0) i0	17293900.00
Molecular weight molecular_weight	28624.0 kDa
Excluded volume excluded_volume	34430 Å³
Envelope volume envelope_volume	49575 Å³
Hydration-shell volume shell_volume	15286 Å³
Envelope diameter envelope_diameter	117.2 Å
Shell Rg shell_rg	32.16 Å
Envelope Rg envelope_rg	34.55 Å
Shape Rg shape_rg	33.69 Å
Total Rg total_rg	33.55 Å
Total atoms total_atoms	1969
Residues n_residues	246
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	115.7 Å
Rg (real space) rg_real	33.30 Å
Rg uncertainty (real space) rg_real_error	1.71 Å
I(0) (real space) i0_real	1.7290e+07
I(0) uncertainty (real space) i0_real_error	3.1350e+05
Rg (reciprocal space) rg_reciprocal	32.80 Å
I(0) (reciprocal space) i0_reciprocal	17290000.0000
Solution quality estimate total_estimate	0.6194
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.9 Å
Skewness Skewness skewness	0.750
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	527400.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.220; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.032; Smooth: 0.357

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Early Endosomal Autoantigen 1
Molecular weight formula_weight	14139.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2025

NNQDERRALLERCLKGEGEIEKLQTKVLELQRKLDNTTAAVQELGRENQSLQIKHTQALNRKWAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACFNDLQG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER
Molecular weight formula_weight	340.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1joca1
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

Domain ID domain_id	d1joca2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.21 — Eea1 homodimerisation domain
Family Family family	h.1.21.1 — Eea1 homodimerisation domain

Domain ID domain_id	d1jocb1
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.1 — FYVE, a phosphatidylinositol-3-phosphate binding domain

Domain ID domain_id	d1jocb2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.21 — Eea1 homodimerisation domain
Family Family family	h.1.21.1 — Eea1 homodimerisation domain

CATH v4.4 (4 domains)

Domain ID domain_id	1jocA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	390 — L1 transposable element, trimerization domain

Domain ID domain_id	1jocA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	1jocB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	390 — L1 transposable element, trimerization domain

Domain ID domain_id	1jocB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	36.528 Å
Unit-cell length b length_b	85.096 Å
Unit-cell length c length_c	88.036 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.2810

fit	/app/data/saxs_computation/jo/1joc/1joc.fit
pddf	/app/data/pr_computation/jo/1joc/1joc.pr.out
profile	/app/data/saxs_computation/jo/1joc/1joc.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Early Endosomal Autoantigen 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction