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1k37

NMR Structure of human Epiregulin

Method: SOLUTION NMR Dmax: 42.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Epiregulin

Homo sapiens

UniProt O14944

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 63–108 Fragment：residues 1-46 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 3.4；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR measurement conditions：pH 3.4；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition：1.5mM Epiregulin, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1.5mM Epiregulin, 100% D2O | 100% 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 1K37 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1K36 NMR Structure of human Epiregulin Deposited 2001-10-02 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 63–108（46 aa） Fragment：residues 1-46
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.4；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR measurement conditions pH 3.4；303 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 1.5mM Epiregulin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1.5mM Epiregulin, 100% D2O | 100% D2O
Resolution not provided
5E8D Crystal structure of human epiregulin in complex with the Fab fragment of murine monoclonal antibody 9E5 Deposited 2015-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–108（71 aa）
Not recorded CL CHLORIDE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；2-(N-morphilino)ethansulfonic acid monohydrate, PEG4000
Resolution 2.50 Å R-free 0.263
5WB7 Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin Deposited 2017-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 56–116（61 aa）
Chain H 56–116（61 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350
Resolution 2.94 Å R-free 0.268
5WB7 Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin Deposited 2017-06-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 56–116（61 aa）
Chain G 56–116（61 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；0.03 M citric acid, 0.07 M Bis-Tris propane, 16% PEG3350
Resolution 2.94 Å R-free 0.268
7LEN Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose Deposited 2021-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate
Resolution 2.90 Å R-free 0.295
7LEN Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with trehalose Deposited 2021-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, with 3% (w/v) D-(+)-trehalose dihydrate
Resolution 2.90 Å R-free 0.295
7LFR Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with spermine Deposited 2021-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 63–110（48 aa）
Chain D 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 MAN alpha-D-mannopyranose × 2 BMA beta-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, 10 mM spermine tetrahydrochloride
Resolution 3.20 Å R-free 0.303
7LFR Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with spermine Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, 10 mM spermine tetrahydrochloride
Resolution 3.20 Å R-free 0.303
7LFR Crystal structure of the epidermal growth factor receptor extracellular region with R84K mutation in complex with epiregulin crystallized with spermine Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；8 mg/ml protein, 100 mM HEPES (pH 7.5), 12% PEG3350, 10 mM spermine tetrahydrochloride
Resolution 3.20 Å R-free 0.303
7LFS Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex with epiregulin Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；8 mg/ml protein, 1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES (pH 7.0), 20% PEG3350
Resolution 3.50 Å R-free 0.315
7LFS Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex with epiregulin Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；8 mg/ml protein, 1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES (pH 7.0), 20% PEG3350
Resolution 3.50 Å R-free 0.315
7LFS Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex with epiregulin Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；8 mg/ml protein, 1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES (pH 7.0), 20% PEG3350
Resolution 3.50 Å R-free 0.315
7LFS Crystal structure of the epidermal growth factor receptor extracellular region with A265V mutation in complex with epiregulin Deposited 2021-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 63–110（48 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；8 mg/ml protein, 1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES (pH 7.0), 20% PEG3350
Resolution 3.50 Å R-free 0.315
8HGP The EREG-bound EGFR/HER2 ectodomain complex Deposited 2022-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 60–108（49 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.53 Å

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EREG_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–46； UniProt 63–108

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 1k37

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k37
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k37
Deposition date deposition_date2001-10-02
Structure title titleNMR Structure of human Epiregulin
Keywords keywordsEGF-like fold, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.16 Å
Radius of gyration Rg (electron density) rg_electron11.64 Å
Forward intensity I(0) i0763431.00
Molecular weight molecular_weight5274.0 kDa
Excluded volume excluded_volume6422 ų
Envelope volume envelope_volume7700 ų
Hydration-shell volume shell_volume6374 ų
Envelope diameter envelope_diameter39.6 Å
Shell Rg shell_rg15.81 Å
Envelope Rg envelope_rg11.93 Å
Shape Rg shape_rg11.69 Å
Total Rg total_rg12.66 Å
Total atoms total_atoms706
Residues n_residues46
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 dmax42.7 Å
Rg (real space) rg_real12.21 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real7.6340e+05
I(0) uncertainty (real space) i0_real_error8.1680e+03
Rg (reciprocal space) rg_reciprocal12.21 Å
I(0) (reciprocal space) i0_reciprocal763400.0000
Solution quality estimate total_estimate0.8528
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.4 Å
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.291
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha129100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.748; Smooth: 0.902
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1k37a_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.11 — EGF/Laminin
Family Family familyg.3.11.1 — EGF-type module

CATH v4.4 (1 domains)

Domain ID domain_id1k37A00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
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8. Citations (1)

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9. Files and Curves (10)