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- PDB-3ho5: Crystal structure of Hedgehog-interacting protein (HHIP) and Soni... -

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Basic information

Entry
Database: PDB / ID: 3ho5
TitleCrystal structure of Hedgehog-interacting protein (HHIP) and Sonic hedgehog (SHH) complex
Components
  • Hedgehog-interacting protein
  • Sonic hedgehog protein
KeywordsSIGNALING PROTEIN / receptor ectodomain / six-bladed-propeller domain / EGF domain / disulfide bond / calcium cation / zinc cation / Cell membrane / EGF-like domain / Glycoprotein / Membrane / Secreted / Autocatalytic cleavage / Developmental protein / Disease mutation / Holoprosencephaly / Hydrolase / Lipoprotein / Microphthalmia / Palmitate / Protease
Function / homology
Function and homology information


regulation of fibroblast growth factor receptor signaling pathway / regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation ...regulation of fibroblast growth factor receptor signaling pathway / regulation of nodal signaling pathway / positive regulation of skeletal muscle cell proliferation / right lung development / left lung development / primary prostatic bud elongation / regulation of mesenchymal cell proliferation involved in prostate gland development / mesenchymal smoothened signaling pathway involved in prostate gland development / positive regulation of sclerotome development / tracheoesophageal septum formation / negative regulation of ureter smooth muscle cell differentiation / positive regulation of ureter smooth muscle cell differentiation / negative regulation of kidney smooth muscle cell differentiation / positive regulation of kidney smooth muscle cell differentiation / morphogen activity / regulation of odontogenesis / positive regulation of mesenchymal cell proliferation involved in ureter development / trunk neural crest cell migration / Formation of lateral plate mesoderm / hindgut morphogenesis / polarity specification of anterior/posterior axis / negative regulation of alpha-beta T cell differentiation / regulation of prostatic bud formation / formation of anatomical boundary / positive regulation of striated muscle cell differentiation / regulation of glial cell proliferation / metanephric mesenchymal cell proliferation involved in metanephros development / ventral midline development / trachea morphogenesis / hedgehog family protein binding / cholesterol-protein transferase activity / HHAT G278V doesn't palmitoylate Hh-Np / telencephalon regionalization / bud outgrowth involved in lung branching / epithelial-mesenchymal cell signaling / Ligand-receptor interactions / lung epithelium development / laminin-1 binding / salivary gland cavitation / negative regulation of cholesterol efflux / spinal cord dorsal/ventral patterning / negative regulation of mesenchymal cell apoptotic process / determination of left/right asymmetry in lateral mesoderm / cell development / spinal cord motor neuron differentiation / negative regulation of T cell differentiation in thymus / positive regulation of T cell differentiation in thymus / establishment of epithelial cell polarity / skeletal muscle cell proliferation / prostate gland development / intermediate filament organization / limb bud formation / embryonic skeletal system development / stem cell development / skeletal muscle fiber differentiation / positive regulation of cerebellar granule cell precursor proliferation / mesenchymal cell apoptotic process / animal organ formation / Activation of SMO / patched binding / hindbrain development / embryonic digestive tract morphogenesis / positive regulation of skeletal muscle tissue development / somite development / ectoderm development / embryonic foregut morphogenesis / negative regulation of dopaminergic neuron differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell proliferation involved in lung development / neuron fate commitment / cerebellar granule cell precursor proliferation / self proteolysis / positive regulation of immature T cell proliferation in thymus / lung lobe morphogenesis / smooth muscle tissue development / dorsal/ventral neural tube patterning / artery development / lymphoid progenitor cell differentiation / positive regulation of astrocyte differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative thymic T cell selection / regulation of stem cell proliferation / pattern specification process / positive regulation of epithelial cell proliferation involved in prostate gland development / male genitalia development / branching involved in salivary gland morphogenesis / Release of Hh-Np from the secreting cell / epithelial cell proliferation involved in prostate gland development / embryonic pattern specification / lung-associated mesenchyme development / intein-mediated protein splicing / glycosaminoglycan binding / Formation of axial mesoderm / thalamus development / dopaminergic neuron differentiation / metanephros development / Developmental Lineage of Pancreatic Acinar Cells / metanephric collecting duct development / positive thymic T cell selection / camera-type eye development
Similarity search - Function
Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module ...Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Muramoyl-pentapeptide Carboxypeptidase; domain 2 - #10 / Hedgehog, N-terminal signalling domain / Hedgehog protein / Hedgehog protein, Hint domain / : / Hint module / Hedgehog amino-terminal signalling domain / Soluble quinoprotein glucose/sorbosone dehydrogenase / 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 / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sonic hedgehog protein / Hedgehog-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsHymowitz, S.G. / Bosanac, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling.
Authors: Bosanac, I. / Maun, H.R. / Scales, S.J. / Wen, X. / Lingel, A. / Bazan, J.F. / de Sauvage, F.J. / Hymowitz, S.G. / Lazarus, R.A.
History
DepositionJun 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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.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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hedgehog-interacting protein
B: Hedgehog-interacting protein
H: Sonic hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5087
Polymers127,2973
Non-polymers2114
Water00
1
A: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1532
Polymers54,0871
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hedgehog-interacting protein
H: Sonic hedgehog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3555
Polymers73,2102
Non-polymers1463
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-58 kcal/mol
Surface area28520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.618, 101.618, 302.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hedgehog-interacting protein / HHIP / HIP


Mass: 54087.246 Da / Num. of mol.: 2 / Fragment: UNP residues 193-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HHIP, HIP, UNQ5825/PRO19644
Plasmid: pENTR/D-TOPO with honeybee melittin secretion signal
Cell line (production host): insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96QV1
#2: Protein Sonic hedgehog protein / SHH / HHG-1 / Sonic hedgehog protein N-product / Sonic hedgehog protein C-product


Mass: 19122.484 Da / Num. of mol.: 1 / Fragment: UNP residues 29-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHH / Plasmid: pET101/D-TOPO (Invitrogen) / Cell line (production host): Rosetta 2 (Novagen) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15465
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Compound detailsTHE SECOND MOLECULE OF SONIC HEDGEHOG PROTEIN WAS CRYSTALLIZED BUT APPEARED TO BE LARGELY ...THE SECOND MOLECULE OF SONIC HEDGEHOG PROTEIN WAS CRYSTALLIZED BUT APPEARED TO BE LARGELY DISORDERED AND WAS NOT INCLUDED IN THE FINAL MODEL. THE SEQUENCE IS: GFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGV KLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSVAAKSGG
Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M bis-Tris propane pH 7.0 and 2.2-2.5 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97839 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97839 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 37181 / Num. obs: 37106 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rsym value: 0.085 / Net I/σ(I): 24.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.589 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1VHH, 3HO4

1vhh

3ho4


Resolution: 3.01→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU B: 40.143 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.342 / ESU R Free: 0.425 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28738 1874 5.1 %RANDOM
Rwork0.23097 ---
all0.23381 35204 --
obs0.23381 35147 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.674 Å2
Baniso -1Baniso -2Baniso -3
1-4.78 Å22.39 Å20 Å2
2--4.78 Å20 Å2
3----7.17 Å2
Refinement stepCycle: LAST / Resolution: 3.01→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8251 0 4 0 8255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218444
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9611395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52951044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34823.68394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.747151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7281558
X-RAY DIFFRACTIONr_chiral_restr0.080.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026462
X-RAY DIFFRACTIONr_nbd_refined0.2040.23517
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.23
X-RAY DIFFRACTIONr_mcbond_it2.1612.55344
X-RAY DIFFRACTIONr_mcangle_it3.63558350
X-RAY DIFFRACTIONr_scbond_it1.9972.53463
X-RAY DIFFRACTIONr_scangle_it3.22353045
LS refinement shellResolution: 3.005→3.066 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.34 103 -
Rwork0.293 2039 -
obs-2142 99.44 %
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)
14.2304-0.8665-1.0872.20350.09955.6920.00351.47070.1007-0.43750.0482-0.0093-0.05210.0539-0.0516-0.5773-0.2034-0.06470.0072-0.113-0.507213.541828.770148.7252
219.02733.4319-14.91860.619-2.690811.6971-0.57420.9847-0.5733-0.5663-0.8648-0.37550.75740.43121.4389-0.07380.08310.07020.9407-0.4029-0.009241.048517.689139.6322
319.5851-3.546811.096910.82792.661625.71910.5733-0.02851.8190.1869-0.5694-0.192-2.4019-0.8979-0.0039-0.39840.04790.1202-0.5158-0.0557-0.273463.257224.082430.9176
43.1991-0.5354-0.45511.91240.87786.3512-0.2454-0.6976-0.31020.58870.19540.04360.74980.26050.05-0.36030.06670.025-0.49690.1228-0.3937.052325.966298.6709
51.8966-0.211-0.16297.97026.37298.3801-0.3586-0.7337-0.11090.423-0.1590.4796-0.5194-0.96570.5176-0.44380.20620.17190.1957-0.1343-0.3473-15.596144.2787108.6657
624.2735-5.14631.16231.41330.633414.1006-0.9788-0.59841.04981.24491.3659-1.086-0.05032.3235-0.3871-0.7689-0.17070.0987-0.4586-0.0418-0.6479-19.924264.3175122.8157
77.43151.31440.4246.0294-0.54075.6755-0.0538-1.17170.19660.80860.0638-0.3688-0.13830.3085-0.010.72950.2086-0.2031.26380.013-0.112317.4734.087136.9189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A214 - 603
2X-RAY DIFFRACTION2A604 - 637
3X-RAY DIFFRACTION3A638 - 669
4X-RAY DIFFRACTION4B214 - 603
5X-RAY DIFFRACTION5B604 - 637
6X-RAY DIFFRACTION6B638 - 669
7X-RAY DIFFRACTION7H38 - 191

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