2ibg

Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog

Method: X-RAY DIFFRACTION Dmax: 127.8 Å Quality: GOOD

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

CG9211-PA

Drosophila melanogaster

UniProt Q9VM64

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 466–677 Fragment:Extracellular FNIII Domains Protein hedgehog × 1 (Q02936) PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 466–677 Fragment:Extracellular FNIII Domains Protein hedgehog × 1 (Q02936) PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 466–677 Fragment:Extracellular FNIII Domains Protein hedgehog × 1 (Q02936) PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 466–677 Fragment:Extracellular FNIII Domains Protein hedgehog × 1 (Q02936) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9VM64_DROME
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–214; UniProt 466–677 Author chain B; PDBConstruct 3–214; UniProt 466–677 Author chain C; PDBConstruct 3–214; UniProt 466–677 Author chain D; PDBConstruct 3–214; UniProt 466–677

Protein hedgehog

Drosophila melanogaster

UniProt Q02936

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 F; UniProt 49–198 Fragment:protein hedgehog N-product CG9211-PA × 1 (Q9VM64) PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 49–198 Fragment:protein hedgehog N-product CG9211-PA × 1 (Q9VM64) PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 49–198 Fragment:protein hedgehog N-product CG9211-PA × 1 (Q9VM64) PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 49–198 Fragment:protein hedgehog N-product CG9211-PA × 1 (Q9VM64) PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.4;293 K;2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.20 Å R-free 0.246

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.

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

View Construct and Data Evidence
UniProt name HH_DROME
Isoform
PDB entities 2
Chains and sequence ranges Author chain E; PDBConstruct 1–150; UniProt 49–198 Author chain F; PDBConstruct 1–150; UniProt 49–198 Author chain G; PDBConstruct 1–150; UniProt 49–198 Author chain H; PDBConstruct 1–150; UniProt 49–198

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 2ibg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ibg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ibg
Deposition date deposition_date2006-09-11
Structure title titleCrystal Structure of Hedgehog Bound to the FNIII Domains of Ihog
Keywords keywordsihog, hedgehog, fibronectin type III, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.68
Radius of gyration Rg (electron density) rg_electron38.17
Forward intensity I(0) i0403003000.00
Molecular weight molecular_weight161130.0 kDa
Excluded volume excluded_volume200960 ų
Envelope volume envelope_volume280620 ų
Hydration-shell volume shell_volume61440 ų
Envelope diameter envelope_diameter129.5
Shell Rg shell_rg44.21
Envelope Rg envelope_rg37.06
Shape Rg shape_rg38.18
Total Rg total_rg38.55
Total atoms total_atoms11355
Residues n_residues1401
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 dmax127.8
Rg (real space) rg_real38.58
Rg uncertainty (real space) rg_real_error0.91
I(0) (real space) i0_real4.0300e+08
I(0) uncertainty (real space) i0_real_error6.3080e+06
Rg (reciprocal space) rg_reciprocal38.65
I(0) (reciprocal space) i0_reciprocal403000000.0000
Solution quality estimate total_estimate0.8523
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary49.9
Skewness Skewness skewness0.332
Kurtosis Kurtosis kurtosis-0.072
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29840000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.776

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd2ibga1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibga2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibga3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ibgb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgb2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ibgc1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgc3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ibgd1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgd2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.2 — Fibronectin type III
Family Family familyb.1.2.1 — Fibronectin type III
Domain ID domain_idd2ibgd3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ibge1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamilyd.65.1 — Hedgehog/DD-peptidase
Family Family familyd.65.1.2 — Hedgehog (development protein), N-terminal signaling domain
Domain ID domain_idd2ibgf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamilyd.65.1 — Hedgehog/DD-peptidase
Family Family familyd.65.1.2 — Hedgehog (development protein), N-terminal signaling domain
Domain ID domain_idd2ibgg_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamilyd.65.1 — Hedgehog/DD-peptidase
Family Family familyd.65.1.2 — Hedgehog (development protein), N-terminal signaling domain
Domain ID domain_idd2ibgh_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.65 — Hedgehog/DD-peptidase
Superfamily Superfamily superfamilyd.65.1 — Hedgehog/DD-peptidase
Family Family familyd.65.1.2 — Hedgehog (development protein), N-terminal signaling domain

CATH v4.4 (12 domains)

Domain ID domain_id2ibgA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgD01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ibgE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id2ibgF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id2ibgG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily10
Domain ID domain_id2ibgH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1380 — Muramoyl-pentapeptide Carboxypeptidase; domain 2
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)