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- PDB-7pgn: HHP-C in complex with glycosaminoglycan mimic SOS -

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Basic information

Entry
Database: PDB / ID: 7pgn
TitleHHP-C 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Jan 31, 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
B: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1129
Polymers105,0092
Non-polymers4,1037
Water66737
1
A: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6025
Polymers52,5051
Non-polymers2,0984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5104
Polymers52,5051
Non-polymers2,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.560, 100.560, 311.880
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: 52504.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HHIP-C, the C-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 / 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.: 4
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris/Bicine pH 8.5, 0.03 M magnesium chloride, 0.03 M calcium chloride, 10% w/v PEG 20 000 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: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→76 Å / Num. obs: 72635 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.022 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 20 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3547 / CC1/2: 0.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFT

2wft


Resolution: 2.4→58.09 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 3664 5.05 %
Rwork0.1904 --
obs0.1922 72499 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→58.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 228 37 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087246
X-RAY DIFFRACTIONf_angle_d1.0759855
X-RAY DIFFRACTIONf_dihedral_angle_d19.2374396
X-RAY DIFFRACTIONf_chiral_restr0.061076
X-RAY DIFFRACTIONf_plane_restr0.0061243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.43160.37691310.36012520X-RAY DIFFRACTION99
2.4316-2.4650.371270.34962652X-RAY DIFFRACTION100
2.5002-2.53750.34191390.31482595X-RAY DIFFRACTION100
2.5375-2.57710.35581400.29812657X-RAY DIFFRACTION100
2.5771-2.61940.33671340.28522558X-RAY DIFFRACTION100
2.6194-2.66460.30271460.27412634X-RAY DIFFRACTION100
2.6646-2.7130.27911470.26822628X-RAY DIFFRACTION100
2.7652-2.82160.341470.27472591X-RAY DIFFRACTION100
2.8216-2.8830.27051320.26412662X-RAY DIFFRACTION100
2.883-2.950.27611670.23782630X-RAY DIFFRACTION100
2.95-3.02380.28751430.23652596X-RAY DIFFRACTION100
3.0238-3.10560.25761470.21712618X-RAY DIFFRACTION100
3.1056-3.19690.27941590.21232599X-RAY DIFFRACTION100
3.1969-3.30010.24661570.20612626X-RAY DIFFRACTION100
3.3001-3.41810.24111510.20492649X-RAY DIFFRACTION100
3.4181-3.55490.25971100.19362668X-RAY DIFFRACTION100
3.5549-3.71670.17961530.17822654X-RAY DIFFRACTION100
3.7167-3.91260.20661420.16962643X-RAY DIFFRACTION100
3.9126-4.15760.20551640.15922661X-RAY DIFFRACTION100
4.1576-4.47860.17461330.14652672X-RAY DIFFRACTION100
4.4786-4.9290.16571460.13552687X-RAY DIFFRACTION100
4.929-5.64180.20081100.15762757X-RAY DIFFRACTION100
5.6418-7.1060.24051170.19072776X-RAY DIFFRACTION100
7.106-58.090.22731600.19772889X-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)
13.08111.0456-0.28753.26011.1754.6621-0.28820.386-0.4652-0.65540.2352-0.13120.5684-0.03470.06850.8852-0.0933-0.01690.43180.00030.600617.3364-34.5372-49.6097
28.52041.33543.04382.910.38155.1405-0.30791.9001-0.3843-1.48350.4249-0.31430.44250.3192-0.10811.7339-0.43120.07371.1287-0.11770.732219.6532-30.0494-70.3505
36.2529-0.05472.06438.37134.47552.8878-0.57361.09790.6026-1.76010.5684-0.4762-0.61910.58250.03881.231-0.16890.08280.74880.0780.62825.7912-17.324-61.1184
43.4133-1.55590.75591.7057-1.49465.89190.09440.19620.2274-0.4721-0.05910.057-0.44230.1618-0.04690.6356-0.02950.00140.29040.01370.516423.0224-13.6838-44.4382
55.61940.53290.57684.03320.74845.0440.0575-0.1874-0.1983-0.11560.06520.27590.4021-0.7489-0.06710.6228-0.1244-0.05970.36530.12530.444212.7561-22.9253-37.713
66.93326.44796.33995.48895.47485.165-0.72090.11070.2132-0.74090.4549-0.1672-1.53050.58380.28271.5545-0.4504-0.17191.0522-0.04010.7748-4.7734-48.3817-66.9316
78.40130.7558-1.01169.35330.89038.7614-0.0330.2273-0.00850.25990.4451-0.7252-0.79262.306-0.42050.6638-0.126-0.0510.8799-0.08210.6-9.3119-67.7171-71.3512
83.34390.02060.21962.5959-0.23276.33230.1417-0.6501-0.16180.4435-0.0652-0.02170.4211-0.1197-0.06360.4635-0.0196-0.0350.5084-0.00390.425725.8908-22.9247-2.5296
94.9830.73480.25244.5208-0.0536.55040.3083-1.63260.76691.5569-0.2570.5614-0.4392-0.2717-0.09891.2084-0.10140.05251.4646-0.18710.654822.1912-14.160115.8641
105.3506-1.98072.41663.0996-0.33729.2122-0.1196-1.6163-0.06670.8637-0.19980.713-0.0309-1.32320.13780.79-0.02120.14221.2774-0.09860.71148.7086-15.98855.1995
114.6697-2.61741.08283.5163-0.06068.30080.0399-0.8317-0.24910.11170.20480.8006-0.1596-1.6622-0.02030.61580.06760.04441.0544-0.01390.7985.0901-15.9551-10.5487
123.3437-0.6817-0.24252.04831.61355.07080.0173-0.6220.36190.6137-0.11931.1087-0.5627-1.74730.02590.6330.19820.16551.2483-0.01780.88011.6345-14.1868-9.2863
132.99160.87720.93541.9142-0.28274.6189-0.0754-0.21090.1605-0.1282-0.02060.0563-0.0731-0.3053-0.00730.50030.05340.01070.5346-0.03170.568818.5625-18.8521-19.136
144.9427-0.64594.31663.249-1.66897.48710.24430.15250.15630.3525-0.7053-0.125-0.62040.57370.4510.9121-0.2162-0.15371.0924-0.05060.776446.7696-9.701610.8544
153.89913.8158-1.07313.7964-0.56769.19350.3135-0.1014-0.85030.1695-0.0549-0.04111.3879-0.3529-0.28390.9606-0.115-0.15690.50380.02630.68466.0157-14.448523.0635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 213 through 359 )
2X-RAY DIFFRACTION2chain 'A' and (resid 360 through 420 )
3X-RAY DIFFRACTION3chain 'A' and (resid 421 through 496 )
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 567 )
5X-RAY DIFFRACTION5chain 'A' and (resid 568 through 606 )
6X-RAY DIFFRACTION6chain 'A' and (resid 607 through 646 )
7X-RAY DIFFRACTION7chain 'A' and (resid 647 through 670 )
8X-RAY DIFFRACTION8chain 'B' and (resid 214 through 381 )
9X-RAY DIFFRACTION9chain 'B' and (resid 382 through 420 )
10X-RAY DIFFRACTION10chain 'B' and (resid 421 through 478 )
11X-RAY DIFFRACTION11chain 'B' and (resid 479 through 508 )
12X-RAY DIFFRACTION12chain 'B' and (resid 509 through 535 )
13X-RAY DIFFRACTION13chain 'B' and (resid 536 through 606 )
14X-RAY DIFFRACTION14chain 'B' and (resid 607 through 640 )
15X-RAY DIFFRACTION15chain 'B' and (resid 641 through 670 )

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