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- PDB-7pgl: HHIP-N, the N-terminal domain of the Hedgehog-Interacting Protein... -

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Basic information

Entry
Database: PDB / ID: 7pgl
TitleHHIP-N, the N-terminal domain of the Hedgehog-Interacting Protein (HHIP), apo-form
ComponentsHedgehog-interacting protein
KeywordsSIGNALING PROTEIN / HHIP / Hedgehog / morphogen / signalling / glycosaminoglycan / cholesterol / palmitate / 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 / negative regulation of apoptotic process / cell surface / signal transduction / zinc ion binding / extracellular region / 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 / Epidermal growth factor-like domain. / EGF-like domain profile. ...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 / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Hedgehog-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGriffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinuskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. ...Griffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinuskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. / Rohatgi, R. / Siebold, C.
Funding support United Kingdom, United States, 7items
OrganizationGrant numberCountry
Cancer Research UKC20724/A14414 United Kingdom
Cancer Research UKC20724/A26752 United Kingdom
European Research Council (ERC)647278 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)HL067773 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM118082 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)GM106078 United States
Wellcome Trust099675/Z/12/Z United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Hedgehog-Interacting Protein is a multimodal antagonist of Hedgehog signalling.
Authors: Griffiths, S.C. / Schwab, R.A. / El Omari, K. / Bishop, B. / Iverson, E.J. / Malinauskas, T. / Dubey, R. / Qian, M. / Covey, D.F. / Gilbert, R.J.C. / Rohatgi, R. / Siebold, C.
History
DepositionAug 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hedgehog-interacting protein


Theoretical massNumber of molelcules
Total (without water)21,0851
Polymers21,0851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Peaks corresponding to HHIP-N monomers (major) and dimers (minor) were observed via SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.050, 59.050, 98.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21085.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HHIP-N, the N-terminal domain of HHIP, recombinantly expressed in and purified from HEK293T cells using the pHLsec vector for mammalian secretion
Source: (gene. exp.) Homo sapiens (human) / Gene: HHIP, HIP, UNQ5825/PRO19644 / Plasmid: pHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96QV1

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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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.0, 0.2 M ammonium chloride, 0.02 M hexamine cobalt (III) chloride and 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.63→50.67 Å / Num. obs: 5640 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Net I/σ(I): 22.3
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 420 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2140: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HHIP-N:SOS

Resolution: 2.63→50.67 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 281 5.02 %
Rwork0.244 --
obs0.2452 5602 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.63→50.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms807 0 0 0 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002834
X-RAY DIFFRACTIONf_angle_d0.5381125
X-RAY DIFFRACTIONf_dihedral_angle_d15.047508
X-RAY DIFFRACTIONf_chiral_restr0.033115
X-RAY DIFFRACTIONf_plane_restr0.003144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6302-3.31370.34871330.2932591X-RAY DIFFRACTION100
3.3137-50.670.25241480.23522730X-RAY DIFFRACTION100
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)
11.17881.3483-0.62519.21051.58541.0186-0.8013-0.76420.2230.83880.94590.6070.97260.1775-0.18412.01310.11840.23421.01120.08820.828212.1618-8.82316.1418
22.55091.54281.28061.10520.21322.39141.1819-0.66010.10751.17461.22470.5105-1.034-0.5892-0.11461.74040.19530.1950.72980.23531.056223.2448-6.21854.5673
32.48070.07891.01365.05770.10265.6412-0.3593-0.00990.02230.67910.13350.46030.0276-0.15230.23550.86110.02180.08910.5850.07030.877514.2893-15.0278-11.9137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 185 )

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