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6td6

Structure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II

Method: ELECTRON MICROSCOPY Dmax: 116.9 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein dispatched

Drosophila melanogaster

UniProt Q9VNJ5

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 × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–1218 Not recorded Protein hedgehog × 1 （Q02936） 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 × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.76 Å

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 6TD6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6TBU Structure of Drosophila melanogaster Dispatched Deposited 2019-11-04 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1218（1218 aa）
Not recorded Y01 CHOLESTEROL HEMISUCCINATE × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å

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

View Construct and Data Evidence
UniProt name DISP_DROME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1218； UniProt 1–1218

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 Other combination Heteromer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–471 Not recorded Protein dispatched × 1 （Q9VNJ5） 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 × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.76 Å

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 6TD6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AT0 17-kDA fragment of hedgehog C-terminal autoprocessing domain Deposited 1997-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 258–402（145 aa） Fragment：17-KDA FRAGMENT OF C-TERMINAL DOMAIN
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.8；20% PEG 3350, 80 mM AMMONIUM SULFATE, 10 mM SODIUM CACODYLATE pH 5.8
Resolution 1.90 Å R-free 0.275
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 49–198（150 aa） Fragment：protein hedgehog N-product
Not recorded 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
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 49–198（150 aa） Fragment：protein hedgehog N-product
Not recorded 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
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 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 H 49–198（150 aa） Fragment：protein hedgehog N-product
Not recorded 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
2IBG Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog Deposited 2006-09-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 49–198（150 aa） Fragment：protein hedgehog N-product
Not recorded 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
6TYY Hedgehog autoprocessing mutant D46H Deposited 2019-08-09 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 258–403（146 aa）
Mutation：D46H 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, HANGING DROP；pH 7.5；298 K；0.1 M Hepes, pH 7.5, 3.4 M sodium formate
Resolution 1.36 Å R-free 0.195

3 other PDB entries and 6 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 B； PDBConstruct 1–471； UniProt 1–471

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 6td6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6td6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6td6
Deposition date deposition_date2019-11-07
Structure title titleStructure of Drosophila melanogaster Dispatched bound to a modified Hedgehog ligand, HhN-C85II
Keywords keywords;RND transporter, Dispatched, Hedgehog, transmembrane domain, ectodomain, cholesteryl hemisuccinate, detergent micelle, digitonin, monomer, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.24 Å
Radius of gyration Rg (electron density) rg_electron35.72 Å
Forward intensity I(0) i0173211000.00
Molecular weight molecular_weight112210.0 kDa
Excluded volume excluded_volume142920 ų
Envelope volume envelope_volume188590 ų
Hydration-shell volume shell_volume45432 ų
Envelope diameter envelope_diameter120.8 Å
Shell Rg shell_rg40.66 Å
Envelope Rg envelope_rg35.15 Å
Shape Rg shape_rg35.66 Å
Total Rg total_rg36.29 Å
Total atoms total_atoms15718
Residues n_residues982
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 dmax116.9 Å
Rg (real space) rg_real36.21 Å
Rg uncertainty (real space) rg_real_error0.89 Å
I(0) (real space) i0_real1.7320e+08
I(0) uncertainty (real space) i0_real_error2.9590e+06
Rg (reciprocal space) rg_reciprocal36.24 Å
I(0) (reciprocal space) i0_reciprocal173200000.0000
Solution quality estimate total_estimate0.9041
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.2 Å
Skewness Skewness skewness0.255
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30450000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.939
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)