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- PDB-6tyy: Hedgehog autoprocessing mutant D46H -

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Basic information

Entry
Database: PDB / ID: 6tyy
TitleHedgehog autoprocessing mutant D46H
ComponentsProtein hedgehog
KeywordsSIGNALING PROTEIN / Hedgehog autoprocessing doamin
Function / homology
Function and homology information


progression of morphogenetic furrow involved in compound eye morphogenesis / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell / Ligand-receptor interactions ...progression of morphogenetic furrow involved in compound eye morphogenesis / terminal cell fate specification, open tracheal system / cytoneme assembly / germ cell attraction / wing disc proximal/distal pattern formation / labial disc development / regulation of cell proliferation involved in compound eye morphogenesis / Bolwig's organ morphogenesis / Release of Hh-Np from the secreting cell / Ligand-receptor interactions / leg disc morphogenesis / Formation and transport of the N-HH ligand / regulation of epithelial cell migration, open tracheal system / morphogenesis of larval imaginal disc epithelium / cell-cell signaling involved in cell fate commitment / Assembly of the 'signalling complexes' / gonadal mesoderm development / compound eye photoreceptor cell differentiation / wing disc pattern formation / negative regulation of homotypic cell-cell adhesion / Hedgehog ligand biogenesis / : / analia development / anterior head segmentation / posterior head segmentation / imaginal disc growth / anterior/posterior lineage restriction, imaginal disc / epithelial cell migration, open tracheal system / trunk segmentation / heart formation / genital disc development / genital disc anterior/posterior pattern formation / compound eye morphogenesis / spiracle morphogenesis, open tracheal system / wing disc anterior/posterior pattern formation / morphogen activity / mucosal immune response / hindgut morphogenesis / segment polarity determination / ventral midline development / foregut morphogenesis / cholesterol-protein transferase activity / imaginal disc-derived wing morphogenesis / compartment pattern specification / glial cell migration / developmental pigmentation / patched binding / germ cell migration / self proteolysis / embryonic pattern specification / positive regulation of protein localization to cell surface / intein-mediated protein splicing / cell fate specification / smoothened signaling pathway / positive regulation of neuroblast proliferation / protein autoprocessing / endocytic vesicle / epidermis development / regulation of mitotic cell cycle / negative regulation of proteolysis / heart development / peptidase activity / cytoplasmic vesicle / regulation of gene expression / Hydrolases; Acting on ester bonds / endosome / calcium ion binding / extracellular space / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLi, H. / Li, Z. / Wang, C. / Callahan, B.P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI140726 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141178 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206592 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: General Base Swap Preserves Activity and Expands Substrate Tolerance in Hedgehog Autoprocessing.
Authors: Zhao, J. / Ciulla, D.A. / Xie, J. / Wagner, A.G. / Castillo, D.A. / Zwarycz, A.S. / Lin, Z. / Beadle, S. / Giner, J.L. / Li, Z. / Li, H. / Banavali, N. / Callahan, B.P. / Wang, C.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein hedgehog


Theoretical massNumber of molelcules
Total (without water)15,9991
Polymers15,9991
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.381, 78.381, 37.351
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein hedgehog


Mass: 15999.280 Da / Num. of mol.: 1 / Mutation: D46H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: hh, CG4637 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02936
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, pH 7.5, 3.4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.36→100 Å / Num. obs: 28219 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.03 / Rrim(I) all: 0.066 / Χ2: 1.136 / Net I/σ(I): 11 / Num. measured all: 131992
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.36-1.382.90.92413670.6240.6421.1340.81296.3
1.38-1.414.10.88913860.6890.4961.0220.52499.8
1.41-1.444.70.75714050.7350.3880.8530.591100
1.44-1.474.80.65613930.8130.3320.7370.743100
1.47-1.54.90.5214210.8390.260.5830.73499.9
1.5-1.534.80.47813990.8580.2450.5390.9499.6
1.53-1.574.80.32314150.9240.1620.3620.57799.8
1.57-1.614.70.26213970.9450.1350.2960.57199.9
1.61-1.664.20.21414110.960.1170.2440.5799.8
1.66-1.714.90.18113950.9770.0890.2020.61599.6
1.71-1.775.10.14914310.9830.0720.1660.66899.9
1.77-1.855.10.1113860.9920.0530.1220.70699.9
1.85-1.934.90.11914180.9880.0590.1331.39199.8
1.93-2.034.90.07414040.9950.0370.0831.14999.9
2.03-2.164.60.0714210.9910.0370.0791.55499.6
2.16-2.334.20.05614060.9930.0320.0651.65899.6
2.33-2.565.30.0514340.9970.0240.0551.788100
2.56-2.935.20.04314250.9980.0210.0482.07399.9
2.93-3.694.90.03714330.9980.0190.0422.4399.7
3.69-1004.60.02914720.9990.0150.0332.14598.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AT0

1at0


Resolution: 1.36→25.656 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.1949 1994 7.08 %
Rwork0.1705 --
obs0.1722 28172 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.69 Å2 / Biso mean: 19.5345 Å2 / Biso min: 7.77 Å2
Refinement stepCycle: final / Resolution: 1.36→25.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 0 0 161 1283
Biso mean---31.26 -
Num. residues----146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3603-1.39440.43621400.4232180796
1.3944-1.43210.40151420.35441842100
1.4321-1.47420.36951420.28361858100
1.4742-1.52180.29841410.22821869100
1.5218-1.57620.25191410.20711864100
1.5762-1.63930.20971420.19311869100
1.6393-1.71380.20071390.1881850100
1.7138-1.80420.2321430.17441881100
1.8042-1.91720.19441410.17761868100
1.9172-2.06520.19371470.15741881100
2.0652-2.27290.17641390.15121858100
2.2729-2.60150.15951410.1661889100
2.6015-3.27650.17791470.15391901100
3.2765-25.6560.15491490.13821941100

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