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- PDB-2ibg: Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog -

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Basic information

Entry
Database: PDB / ID: 2ibg
TitleCrystal Structure of Hedgehog Bound to the FNIII Domains of Ihog
Components
  • CG9211-PA
  • Protein hedgehog
KeywordsPROTEIN BINDING / ihog / hedgehog / fibronectin type III
Function / homology
Function and homology information


maintenance of protein location in extracellular region / Myogenesis / 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 ...maintenance of protein location in extracellular region / Myogenesis / 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 / cuticle pattern formation / Release of Hh-Np from the secreting cell / Ligand-receptor interactions / leg disc morphogenesis / Formation and transport of the N-HH ligand / cytoneme / 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 / Signaling by ROBO receptors / : / wing disc pattern formation / negative regulation of homotypic cell-cell adhesion / Hedgehog ligand biogenesis / imaginal disc growth / : / analia development / anterior head segmentation / posterior head segmentation / 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 / compound eye development / segment polarity determination / ventral midline development / hedgehog family protein binding / foregut morphogenesis / cholesterol-protein transferase activity / homotypic cell-cell adhesion / imaginal disc-derived wing morphogenesis / compartment pattern specification / segment 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 / coreceptor activity / regulation of mitotic cell cycle / negative regulation of proteolysis / cell-cell adhesion / heparin binding / heart development / peptidase activity / cytoplasmic vesicle / regulation of gene expression / Hydrolases; Acting on ester bonds / endosome / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / Hint module / Hedgehog amino-terminal signalling domain / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / 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 / Immunoglobulin domain / Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein hedgehog / Interference hedgehog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMcLellan, J.S. / Leahy, D.J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structure of a heparin-dependent complex of Hedgehog and Ihog.
Authors: McLellan, J.S. / Yao, S. / Zheng, X. / Geisbrecht, B.V. / Ghirlando, R. / Beachy, P.A. / Leahy, D.J.
History
DepositionSep 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG9211-PA
B: CG9211-PA
C: CG9211-PA
D: CG9211-PA
E: Protein hedgehog
F: Protein hedgehog
G: Protein hedgehog
H: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,38720
Polymers166,2478
Non-polymers1,14012
Water5,206289
1
A: CG9211-PA
F: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8475
Polymers41,5622
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CG9211-PA
E: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0377
Polymers41,5622
Non-polymers4755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CG9211-PA
H: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8475
Polymers41,5622
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CG9211-PA
G: Protein hedgehog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6573
Polymers41,5622
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.354, 70.003, 155.695
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CG9211-PA / GH03927p


Mass: 24290.354 Da / Num. of mol.: 4 / Fragment: Extracellular FNIII Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: iHog, CG9211 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9VM64
#2: Protein
Protein hedgehog


Mass: 17271.426 Da / Num. of mol.: 4 / Fragment: protein hedgehog N-product
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: hh / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q02936
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 82885 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.6
Reflection shellHighest resolution: 2.2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2IBB PDB Entry 1VHH

2ibb

1vhh


Resolution: 2.2→37.68 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 14.824 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3864 5.1 %RANDOM
Rwork0.198 ---
obs0.2 76254 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.719 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20.31 Å2
2---1.49 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11295 0 60 289 11644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211640
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.96415802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84451387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83323.148540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.785151948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1041589
X-RAY DIFFRACTIONr_chiral_restr0.090.21683
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028891
X-RAY DIFFRACTIONr_nbd_refined0.2050.25162
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2582
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.217
X-RAY DIFFRACTIONr_mcbond_it0.6791.57209
X-RAY DIFFRACTIONr_mcangle_it1.104211373
X-RAY DIFFRACTIONr_scbond_it1.66935141
X-RAY DIFFRACTIONr_scangle_it2.564.54429
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 264 -
Rwork0.271 4722 -
obs-4986 81.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04040.536-0.62061.8211-0.39782.050.0199-0.054-0.08460.0986-0.0019-0.078-0.09540.0475-0.018-0.18290.0373-0.0425-0.134-0.0328-0.013168.215935.1823152.7672
21.940.0560.01551.5032-0.35442.05050.05790.11640.091-0.11310.0122-0.08770.05540.1137-0.0701-0.101-0.05080.033-0.1115-0.0404-0.088568.828850.052281.8151
32.50740.0618-0.47731.4601-0.02142.3298-0.01180.1411-0.2015-0.04630.07880.126-0.0919-0.0361-0.067-0.1063-0.0373-0.0284-0.16810.0406-0.061343.815538.624981.6169
42.05550.30970.1741.76470.80032.1349-0.0093-0.13460.11710.06710.02470.10770.0148-0.047-0.0153-0.16840.05330.0134-0.09840.0543-0.049943.603449.1758152.8744
52.6156-1.07451.18273.1027-0.63983.815-0.1916-0.16160.18790.3938-0.0424-0.493-0.45960.3410.2339-0.035-0.1195-0.0348-0.0805-0.0816-0.073876.321561.5683117.2588
62.4940.66432.323310.435910.298614.30260.18450.7895-0.3535-0.6471.4964-1.7013-0.13211.9097-1.6809-0.14660.01370.06110.2165-0.42660.126372.278420.6329119.7415
74.06871.0977-0.61396.1638-0.53583.20690.13920.51020.2037-0.59460.1870.8515-0.7017-0.7782-0.32630.06130.2419-0.00860.03350.1743-0.114939.819164.9075120.5838
83.12571.0168-3.63856.2976-5.291110.76990.1494-0.2777-0.04230.46560.04820.5233-0.2789-0.182-0.1976-0.1803-0.08160.0022-0.11360.194-0.113335.845124.5987115.4896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA464 - 6771 - 214
22BB464 - 6761 - 213
33CC464 - 6761 - 213
44DD464 - 6761 - 213
55EE100 - 2482 - 150
66FF99 - 2461 - 148
77GG99 - 2471 - 149
88HH100 - 2482 - 150

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