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- PDB-3k7g: Crystal structure of the Indian Hedgehog N-terminal signalling domain -

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Basic information

Entry
Database: PDB / ID: 3k7g
TitleCrystal structure of the Indian Hedgehog N-terminal signalling domain
ComponentsIndian hedgehog protein
KeywordsSIGNALING PROTEIN / alpha+beta sandwich / Autocatalytic cleavage / Cell membrane / Developmental protein / Disease mutation / Glycoprotein / Hydrolase / Lipoprotein / Membrane / Palmitate / Protease / Secreted
Function / homology
Function and homology information


vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np ...vitelline membrane formation / negative regulation of eye pigmentation / camera-type eye photoreceptor cell fate commitment / chondrocyte differentiation involved in endochondral bone morphogenesis / embryonic skeletal joint development / Formation of lateral plate mesoderm / negative regulation of alpha-beta T cell differentiation / embryonic camera-type eye morphogenesis / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / RUNX2 regulates chondrocyte maturation / Ligand-receptor interactions / proteoglycan metabolic process / negative regulation of immature T cell proliferation in thymus / chondrocyte proliferation / embryonic digestive tract morphogenesis / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / retinal pigment epithelium development / epithelial cell-cell adhesion / Activation of SMO / patched binding / somite development / embryonic pattern specification / smooth muscle tissue development / epithelial cell morphogenesis / self proteolysis / head morphogenesis / Release of Hh-Np from the secreting cell / intein-mediated protein splicing / positive regulation of smoothened signaling pathway / pancreas development / negative regulation of chondrocyte differentiation / regulation of growth / Class B/2 (Secretin family receptors) / positive regulation of mesenchymal cell proliferation / positive regulation of alpha-beta T cell differentiation / cell fate specification / embryonic digit morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / heart looping / protein autoprocessing / positive regulation of collagen biosynthetic process / neuron development / maternal process involved in female pregnancy / bone resorption / response to mechanical stimulus / cell maturation / extracellular matrix / positive regulation of epithelial cell proliferation / skeletal system development / liver regeneration / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / osteoblast differentiation / cell-cell signaling / response to estradiol / peptidase activity / regulation of gene expression / in utero embryonic development / Hydrolases; Acting on ester bonds / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
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 ...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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Indian hedgehog protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHe, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
CitationJournal: To be Published
Title: Crystal structure of the Indian Hedgehog N-terminal signalling domain
Authors: He, Y.-X. / Kang, Y. / Zhang, W.J. / Yu, J. / Ma, G. / Zhou, C.-Z.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
B: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6577
Polymers21,1161
Non-polymers5426
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.660, 53.350, 35.440
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-247-

HOH

21B-282-

HOH

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Components

#1: Protein Indian hedgehog protein / IHH / HHG-2


Mass: 21115.633 Da / Num. of mol.: 1 / Fragment: Indian hedgehog protein N-product
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) / References: UniProt: Q14623
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→23.9 Å / Num. obs: 32115 / % possible obs: 99.7 % / Redundancy: 2.7 % / Biso Wilson estimate: 11.73 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 22.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 10 / Num. unique all: 4650 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHH

1vhh


Resolution: 1.5→21.311 Å / Occupancy max: 1 / Occupancy min: 0.56 / FOM work R set: 0.906 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 16.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 1627 5.07 %RANDOM
Rwork0.1721 30480 --
obs0.1727 32107 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.135 Å2 / ksol: 0.427 e/Å3
Displacement parametersBiso max: 47.89 Å2 / Biso mean: 13.648 Å2 / Biso min: 4.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.628 Å20 Å20.441 Å2
2---0.044 Å2-0 Å2
3----1.584 Å2
Refinement stepCycle: LAST / Resolution: 1.5→21.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 27 248 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051311
X-RAY DIFFRACTIONf_angle_d1.0731771
X-RAY DIFFRACTIONf_dihedral_angle_d16.711481
X-RAY DIFFRACTIONf_chiral_restr0.077181
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54410.19591300.1762519X-RAY DIFFRACTION99
1.5441-1.5940.18511270.16632500X-RAY DIFFRACTION100
1.594-1.65090.17951480.16392525X-RAY DIFFRACTION100
1.6509-1.7170.2131390.17592543X-RAY DIFFRACTION100
1.717-1.79510.19151240.16492532X-RAY DIFFRACTION100
1.7951-1.88970.17421400.15372553X-RAY DIFFRACTION100
1.8897-2.0080.18291220.15172562X-RAY DIFFRACTION100
2.008-2.16290.15241410.1472530X-RAY DIFFRACTION100
2.1629-2.38030.16151160.15922575X-RAY DIFFRACTION100
2.3803-2.72410.19941400.1762548X-RAY DIFFRACTION100
2.7241-3.42980.18611400.16732547X-RAY DIFFRACTION100
3.4298-21.31260.1461600.15712546X-RAY DIFFRACTION98

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