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- PDB-3n1o: Crystal structure of IhhN -

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Basic information

Entry
Database: PDB / ID: 3n1o
TitleCrystal structure of IhhN
ComponentsIndian hedgehog protein
KeywordsPROTEIN BINDING / Binding Sites / Calcium / Cell Adhesion Molecules / Cell Cycle Proteins / Cell Line / Conserved Sequence / Fibronectins / Hedgehog Proteins / Immunoglobulin G / Membrane Glycoproteins / Membrane Proteins / Tertiary / Receptors / Cell Surface / Sequence Homology / Signal Transduction / Tumor Suppressor Proteins
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 / chondrocyte proliferation / proteoglycan metabolic process / negative regulation of immature T cell proliferation in thymus / negative regulation of T cell differentiation in thymus / retinal pigment epithelium development / positive regulation of T cell differentiation in thymus / epithelial cell-cell adhesion / Activation of SMO / patched binding / embryonic digestive tract morphogenesis / somite development / smooth muscle tissue development / epithelial cell morphogenesis / self proteolysis / head morphogenesis / embryonic pattern specification / 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 / Class B/2 (Secretin family receptors) / regulation of growth / cell fate specification / positive regulation of alpha-beta T cell differentiation / positive regulation of mesenchymal cell proliferation / smoothened signaling pathway / branching involved in blood vessel morphogenesis / embryonic digit morphogenesis / heart looping / protein autoprocessing / neuron development / maternal process involved in female pregnancy / positive regulation of collagen biosynthetic process / response to mechanical stimulus / cell maturation / bone resorption / extracellular matrix / skeletal system development / liver regeneration / positive regulation of epithelial cell proliferation / Hedgehog ligand biogenesis / Hedgehog 'on' state / multicellular organism growth / osteoblast differentiation / response to estradiol / cell-cell signaling / 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 / 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 / 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: 2.55 Å
AuthorsKavran, J.M. / Leahy, D.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: All mammalian Hedgehog proteins interact with cell adhesion molecule, down-regulated by oncogenes (CDO) and brother of CDO (BOC) in a conserved manner.
Authors: Kavran, J.M. / Ward, M.D. / Oladosu, O.O. / Mulepati, S. / Leahy, D.J.
History
DepositionMay 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

Downloads & links

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Assembly

Deposited unit
A: Indian hedgehog protein
B: Indian hedgehog protein
C: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6047
Polymers57,3673
Non-polymers2364
Water2,144119
1
A: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1882
Polymers19,1221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1882
Polymers19,1221
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Indian hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2283
Polymers19,1221
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.965, 67.965, 243.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-214-

HOH

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Components

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


Mass: 19122.406 Da / Num. of mol.: 3 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IHH / Production host: Escherichia coli (E. coli) / References: UniProt: Q14623
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 1M NaCitrate, 100mM Cacodylate, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 18164

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→30.99 Å / SU ML: 0.92 / σ(F): 1.35 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 935 5.15 %
Rwork0.1962 --
obs0.1995 18151 92.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.339 Å2 / ksol: 0.418 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5584 Å20 Å20 Å2
2---1.5584 Å2-0 Å2
3---3.1167 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 4 119 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043711
X-RAY DIFFRACTIONf_angle_d0.8515011
X-RAY DIFFRACTIONf_dihedral_angle_d18.0431374
X-RAY DIFFRACTIONf_chiral_restr0.057523
X-RAY DIFFRACTIONf_plane_restr0.003657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.68310.34131310.22642498X-RAY DIFFRACTION96
2.6831-2.85110.32161310.22372523X-RAY DIFFRACTION97
2.8511-3.07110.25171350.22252496X-RAY DIFFRACTION96
3.0711-3.37980.29661440.1882404X-RAY DIFFRACTION92
3.3798-3.86810.22981460.16812318X-RAY DIFFRACTION89
3.8681-4.87030.20351250.15092347X-RAY DIFFRACTION87
4.8703-30.99270.25621230.21012630X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 5.5508 Å / Origin y: -29.1867 Å / Origin z: 41.9078 Å
111213212223313233
T0.0721 Å2-0.0027 Å20.0034 Å2-0.0889 Å20.0152 Å2--0.0903 Å2
L0.1827 °2-0.0023 °2-0.0659 °2-0.0496 °2-0.0542 °2--0.4617 °2
S0.0079 Å °0.0029 Å °0.0174 Å °0.0266 Å °-0.0043 Å °0.0269 Å °0.0621 Å °0.0179 Å °-0 Å °
Refinement TLS groupSelection details: all

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