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1f8h

STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFR

Method: SOLUTION NMR Dmax: 36.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15

Homo sapiens

UniProt P42566

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 121–215 Fragment：RESIDUES 121-218 OF HUMAN EPS15 PTGSSSTNPFR × 1 CA CALCIUM ION × 1 SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：1 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride | 10%/90% D2O/H2O NMR sample composition：1 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride | 99.999% D2O NMR sample composition：0.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride | 10%/90% D2O/H2O NMR sample composition：0.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride | 10%/90% D2O/H2O 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 1F8H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C07 STRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 Deposited 1999-07-14 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 217–311（95 aa） Fragment：EPS15 HOMOLOGY (EH) DOMAIN 3
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.8；298 K；Ionic strength (raw mmCIF value) 100mM KCL, 2mM CACL2, 2mM NAN3；Pressure AMBIENT
NMR sample composition 0.5-1MM EH3; 20MM D-TRIS, 100MM KCL, 2MM CACL2, 2MM NAN3, 0.1MM D-DTT; 95% H2O, 5% D2O
Resolution not provided
1EH2 STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15, NMR, 20 STRUCTURES Deposited 1998-07-10 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 121–218（98 aa） Fragment：EPS15 HOMOLOGY (EH) DOMAIN 2, RESIDUES 121-218
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120 MILLIMOLAR；Pressure ATMOSPHERIC
NMR sample composition H2O AND D2O
Resolution not provided
1FF1 STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFL Deposited 2000-07-24 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 121–215（95 aa） Fragment：SECOND EH DOMAIN
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure AMBIENT
NMR sample composition 1 MM {15N}-EH2 AND 5 MM PEPTIDE, 20 MM PERDEUTERATED TRIS, 100 MM POTASSIUM CHLORIDE, 1 MM PERDEUTERATED DTT, 1 MM SODIUM AZIDE, 2 MM CALCIUM CHLORIDE | 90% H2O/10% D2O
NMR sample composition 1 MM {15N}-EH2 AND 5 MM PEPTIDE, 20 MM PERDEUTERATED TRIS, 100 MM POTASSIUM CHLORIDE, 1 MM PERDEUTERATED DTT, 1 MM SODIUM AZIDE, 2 MM CALCIUM CHLORIDE | 100% D2O
Resolution not provided
2JXC Structure of the EPS15-EH2 Stonin2 Complex Deposited 2007-11-12 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 121–215（95 aa） Fragment：EH 2 domain
Not recorded CA CALCIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；295 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition 0.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 100% D2O | 100% D2O
NMR sample composition 0.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 100% D2O | 100% D2O
NMR sample composition 0.6 mM EH2, 0.6 mM Stonin peptide, 2 mM CA, 100% D2O | 100% D2O
Resolution not provided
4RH5 Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 peptide Deposited 2014-10-01 Different construct Different mutation/modification 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 846–854（9 aa） Fragment：PTYR849 peptide (UNP RESIDUES 846-854)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.203
4RH9 Crystal structure of PTPN3 (PTPH1) H812F, M883G mutant in complex with Eps15 pTyr849 peptide Deposited 2014-10-01 Different construct Different mutation/modification 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 846–854（9 aa） Fragment：pTyr849 peptide (UNP RESIDUES 846-854)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.226
4RHG Crystal structure of PTPN3 (PTPH1) D811E, C842S mutant in complex with Eps15 pTyr849 peptide Deposited 2014-10-02 Different construct Different mutation/modification 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 846–854（9 aa） Fragment：pTyr849 peptide (UNP RESIDUES 846-854)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.58 Å R-free 0.209
4S0G Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 P850V peptide Deposited 2014-12-31 Different construct Different mutation/modification 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 846–854（9 aa） Fragment：Phosphotyrosine 849 peptide, UNP residues 846-854
Mutation：P850V Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 26% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.72 Å R-free 0.229
5JP2 Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide Deposited 2016-05-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 615–637（23 aa） Fragment：UNP Residues 615-637
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM Bis-Tris propane pH, 6.0, 200 mM sodium citrate, 22% PEG 3350 and 10 mM DTT Crystals were cryopretetcted in 22% glycerol before flash cooling
Resolution 2.40 Å R-free 0.234
5JP2 Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide Deposited 2016-05-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 615–637（23 aa） Fragment：UNP Residues 615-637
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM Bis-Tris propane pH, 6.0, 200 mM sodium citrate, 22% PEG 3350 and 10 mM DTT Crystals were cryopretetcted in 22% glycerol before flash cooling
Resolution 2.40 Å R-free 0.234

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EP15_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–95； UniProt 121–215

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 1f8h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1f8h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1f8h
Deposition date deposition_date2000-06-30
Structure title titleSTRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFR
Keywords keywordsCOMPLEX, EH DOMAIN, NPF, CALCIUM BINDING, SIGNALING DOMAIN, EF-HAND, 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_guinier12.31 Å
Radius of gyration Rg (electron density) rg_electron12.10 Å
Forward intensity I(0) i0626599000.00
Molecular weight molecular_weight225820.0 kDa
Excluded volume excluded_volume287740 ų
Envelope volume envelope_volume21014 ų
Hydration-shell volume shell_volume12821 ų
Envelope diameter envelope_diameter45.0 Å
Shell Rg shell_rg19.70 Å
Envelope Rg envelope_rg13.95 Å
Shape Rg shape_rg12.07 Å
Total Rg total_rg12.37 Å
Total atoms total_atoms31859
Residues n_residues2020
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 dmax36.8 Å
Rg (real space) rg_real12.19 Å
Rg uncertainty (real space) rg_real_error0.22 Å
I(0) (real space) i0_real6.2660e+08
I(0) uncertainty (real space) i0_real_error6.8220e+06
Rg (reciprocal space) rg_reciprocal12.20 Å
I(0) (reciprocal space) i0_reciprocal626600000.0000
Solution quality estimate total_estimate0.8090
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.8 Å
Skewness Skewness skewness-0.073
Kurtosis Kurtosis kurtosis-0.453
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha219600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.000
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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_idd1f8ha_
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.6 — Eps15 homology domain (EH domain)

CATH v4.4 (1 domains)

Domain ID domain_id1f8hA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
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8. Citations (1)

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9. Files and Curves (10)