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- PDB-3ho3: Crystal structure of Hedgehog-interacting protein (HHIP) -

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Basic information

Entry
Database: PDB / ID: 3ho3
TitleCrystal structure of Hedgehog-interacting protein (HHIP)
ComponentsHedgehog-interacting protein
KeywordsSIGNALING PROTEIN / receptor ectodomain / six-bladed-propeller domain / EGF domain / disulfide bond / Cell membrane / EGF-like domain / Glycoprotein / Membrane / Secreted
Function / homology
Function and homology information


regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / Ligand-receptor interactions / dorsal/ventral pattern formation / skeletal system morphogenesis / ciliary membrane / epithelial tube branching involved in lung morphogenesis / neuroblast proliferation / negative regulation of signal transduction / negative regulation of smoothened signaling pathway ...regulation of fibroblast growth factor receptor signaling pathway / hedgehog family protein binding / Ligand-receptor interactions / dorsal/ventral pattern formation / skeletal system morphogenesis / ciliary membrane / epithelial tube branching involved in lung morphogenesis / neuroblast proliferation / negative regulation of signal transduction / negative regulation of smoothened signaling pathway / cell surface / signal transduction / extracellular region / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Soluble quinoprotein glucose/sorbosone dehydrogenase / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / Laminin / Laminin ...Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Folate receptor-like / Folate receptor family / Soluble quinoprotein glucose/sorbosone dehydrogenase / 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 / Mainly Beta
Similarity search - Domain/homology
Hedgehog-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBosanac, I. / Hymowitz, S.G.
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 / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hedgehog-interacting protein


Theoretical massNumber of molelcules
Total (without water)54,0871
Polymers54,0871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.230, 118.011, 126.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 54087.246 Da / Num. of mol.: 1 / Fragment: UNP residues 193-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HHIP, HHIP ORFNames: UNQ5825/PRO19644, 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
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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium acetate, 0.2 M ammonium sulfate, 22-24% PEG 4000 and 1-2% dioxane, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2006
Details: vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror
RadiationMonochromator: LN2 cooled double-crystal silicon (111) monochromator with toroidal focusing M2 mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 14785 / Num. obs: 14755 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.089 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.491 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HO4

3ho4


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 45.17 / SU ML: 0.386 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 4.696 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29153 722 5 %RANDOM
Rwork0.23968 ---
all0.24229 13892 --
obs0.24229 13746 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.581 Å2
Baniso -1Baniso -2Baniso -3
1--7.28 Å20 Å20 Å2
2---2.01 Å20 Å2
3---9.29 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 0 0 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213509
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9674750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22523.681163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.2315576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3041524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022710
X-RAY DIFFRACTIONr_nbd_refined0.1990.21437
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0470.22
X-RAY DIFFRACTIONr_mcbond_it1.7952.52233
X-RAY DIFFRACTIONr_mcangle_it3.05853502
X-RAY DIFFRACTIONr_scbond_it1.5222.51412
X-RAY DIFFRACTIONr_scangle_it2.50451248
LS refinement shellResolution: 2.9→2.959 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.422 25 -
Rwork0.284 702 -
obs-727 85.93 %
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)
13.54560.7735-0.80543.8961-0.79283.3257-0.196-0.1070.0139-0.09780.03880.0436-0.2398-0.61610.1573-0.3238-0.0039-0.002-0.1289-0.0593-0.305122.0797-19.09918.4977
22.3906-0.4142-2.29153.20322.02818.1305-0.3345-0.2811-0.9481-0.9224-0.0301-0.89650.74660.36810.36470.0261-0.27020.2323-0.1646-0.21370.332922.3908-48.22358.8538
320.00065.06763.781317.24733.699313.28260.0526-0.3156-0.5308-0.1429-0.1871-0.19380.324-0.0040.1346-0.1168-0.06230.2103-0.2693-0.01120.58486.7432-68.274710.3641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A215 - 603
2X-RAY DIFFRACTION2A604 - 637
3X-RAY DIFFRACTION3A638 - 669

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