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

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Basic information

Entry
Database: PDB / ID: 7pgk
TitleHHIP-N, the N-terminal domain of the Hedgehog-Interacting Protein (HHIP), in complex with glycosaminoglycan mimic SOS
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
sucrose octasulfate / Hedgehog-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0682
Polymers21,0851
Non-polymers9831
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 area310 Å2
ΔGint-5 kcal/mol
Surface area8770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.240, 60.240, 108.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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
#2: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M imidazole/MES pH 6.5, 0.1 M carboxylic acids (0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M sodium oxamate and 0.02 M potassium sodium tartrate), 10% ...Details: 0.1 M imidazole/MES pH 6.5, 0.1 M carboxylic acids (0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M sodium oxamate and 0.02 M potassium sodium tartrate), 10% w/v PEG 20000 and 20% v/v PEG MME 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.75→54.2 Å / Num. obs: 5609 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 107.32 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Net I/σ(I): 12
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 534 / CC1/2: 0.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
xia2data reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→54 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.845 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.592 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.698 / SU Rfree Blow DPI: 0.343 / SU Rfree Cruickshank DPI: 0.331
RfactorNum. reflection% reflectionSelection details
Rfree0.286 288 5.13 %RANDOM
Rwork0.267 ---
obs0.268 5609 100 %-
Displacement parametersBiso mean: 102.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.9205 Å20 Å20 Å2
2---3.9205 Å20 Å2
3---7.8409 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: 1 / Resolution: 2.75→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 55 0 1019
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071049HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91425HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d492SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes20HARMONIC2
X-RAY DIFFRACTIONt_gen_planes143HARMONIC5
X-RAY DIFFRACTIONt_it1049HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.94
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion125SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1074SEMIHARMONIC4
LS refinement shellResolution: 2.75→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.271 -5.15 %
Rwork0.284 1456 -
all0.283 1535 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -15.6739 Å / Origin y: -12.329 Å / Origin z: -22.0729 Å
111213212223313233
T-0.2355 Å20.0946 Å20.0364 Å2-0.1204 Å20.0731 Å2---0.0777 Å2
L4.5765 °23.2835 °24.0403 °2-3.3743 °23.833 °2--6.2208 °2
S-0.0007 Å °-0.1305 Å °-0.0218 Å °0.1292 Å °0.0486 Å °-0.0314 Å °0.0449 Å °-0.0587 Å °-0.0479 Å °
Refinement TLS groupSelection details: { A|36 - A|184 }

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