5wb7

Crystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin

Method: X-RAY DIFFRACTION Dmax: 170.5 Å Quality: GOOD

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

Epidermal growth factor receptor

Homo sapiens

UniProt P00533

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 25–525 Chain D; UniProt 25–525 Not recorded Proepiregulin × 2 (O14944) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2 Other combination Heteromer Protein × 4 其他Polymer 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 25–525 Chain C; UniProt 25–525 Not recorded Proepiregulin × 2 (O14944) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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.

383 other PDB entries and 564 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform P00533-4
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–501; UniProt 25–525 Author chain B; PDBConstruct 1–501; UniProt 25–525 Author chain C; PDBConstruct 1–501; UniProt 25–525 Author chain D; PDBConstruct 1–501; UniProt 25–525

Proepiregulin

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 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 56–116 Chain H; UniProt 56–116 Not recorded Epidermal growth factor receptor × 2 (P00533) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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
2 Other combination Heteromer Protein × 4 其他Polymer 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 56–116 Chain G; UniProt 56–116 Not recorded Epidermal growth factor receptor × 2 (P00533) ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 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

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.

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EREG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 2–62; UniProt 56–116 Author chain F; PDBConstruct 2–62; UniProt 56–116 Author chain G; PDBConstruct 2–62; UniProt 56–116 Author chain H; PDBConstruct 2–62; UniProt 56–116

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 5wb7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wb7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wb7
Deposition date deposition_date2017-06-28
Structure title titleCrystal structure of the epidermal growth factor receptor extracellular region in complex with epiregulin
Keywords keywordsReceptor tyrosine kinase, growth factor, signaling, membrane protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier48.60
Radius of gyration Rg (electron density) rg_electron48.60
Forward intensity I(0) i0976918000.00
Molecular weight molecular_weight244910.0 kDa
Excluded volume excluded_volume300810 ų
Envelope volume envelope_volume436600 ų
Hydration-shell volume shell_volume76924 ų
Envelope diameter envelope_diameter171.8
Shell Rg shell_rg50.61
Envelope Rg envelope_rg47.52
Shape Rg shape_rg48.61
Total Rg total_rg48.62
Total atoms total_atoms17062
Residues n_residues2186
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax170.5
Rg (real space) rg_real48.73
Rg uncertainty (real space) rg_real_error1.83
I(0) (real space) i0_real9.7690e+08
I(0) uncertainty (real space) i0_real_error2.0200e+07
Rg (reciprocal space) rg_reciprocal48.60
I(0) (reciprocal space) i0_reciprocal976700000.0000
Solution quality estimate total_estimate0.8585
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.6
Skewness Skewness skewness0.424
Kurtosis Kurtosis kurtosis-0.166
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha61730000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.791

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5wb7e_
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
Domain ID domain_idd5wb7f_
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
Domain ID domain_idd5wb7g_
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
Domain ID domain_idd5wb7h_
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 (11 domains)

Domain ID domain_id5wb7A01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id5wb7A02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id5wb7B01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id5wb7B02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id5wb7C01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id5wb7D01
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id5wb7D02
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology20 — 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
Homologous superfamily homologous superfamily20 — Receptor L-domain
Domain ID domain_id5wb7E00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id5wb7F00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id5wb7G00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin
Domain ID domain_id5wb7H00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology25 — Laminin
Homologous superfamily homologous superfamily10 — Laminin

8. Citations (1)

9. Files and Curves (10)