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- PDB-7pgm: HHIP-C in complex with heparin -

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Basic information

Entry
Database: PDB / ID: 7pgm
TitleHHIP-C in complex with heparin
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: 2.7 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
C: Hedgehog-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,8414
Polymers157,5143
Non-polymers2,3281
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Large clusters of HHIP-C are observed to be assembled in the presence of heparin via sedimentation velocity analytical ultracentrifugation experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint17 kcal/mol
Surface area62520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.637, 105.252, 148.433
Angle α, β, γ (deg.)90.00, 95.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 52504.500 Da / Num. of mol.: 3
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 / Plasmid: pHLsec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96QV1
#2: Polysaccharide 2-O-sulfo-alpha-L-idopyranuronic acid-(1-3)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-3)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 2327.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,8,7/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O]/1-2-1-2-1-2-1-2/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g3-h1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(3+1)][a-L-IdopA2SO3]{}}}}}}}}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: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-Tris pH 6.5, 0.2 M sodium citrate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.7→147.6 Å / Num. obs: 71834 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Net I/σ(I): 12.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3487 / CC1/2: 0.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2645: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFT

2wft


Resolution: 2.7→84.855 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 3635 5.13 %
Rwork0.2158 --
obs0.217 70890 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→84.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10168 0 141 0 10309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410572
X-RAY DIFFRACTIONf_angle_d0.86614323
X-RAY DIFFRACTIONf_dihedral_angle_d18.1786420
X-RAY DIFFRACTIONf_chiral_restr0.0511555
X-RAY DIFFRACTIONf_plane_restr0.0051843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73540.53551340.47362314X-RAY DIFFRACTION90
2.7354-2.77290.50431370.46912466X-RAY DIFFRACTION94
2.7729-2.81250.45821220.44782490X-RAY DIFFRACTION96
2.8125-2.85450.4341510.41182515X-RAY DIFFRACTION97
2.8991-2.94660.39031420.38322613X-RAY DIFFRACTION98
2.9466-2.99740.41191340.37152509X-RAY DIFFRACTION98
2.9974-3.05190.39471390.33812615X-RAY DIFFRACTION99
3.0519-3.11060.3341390.31632592X-RAY DIFFRACTION99
3.1106-3.17410.32641470.30942575X-RAY DIFFRACTION99
3.1741-3.24320.33271560.31772601X-RAY DIFFRACTION99
3.2432-3.31860.35921250.27782598X-RAY DIFFRACTION99
3.3186-3.40160.28671440.24522589X-RAY DIFFRACTION100
3.4016-3.49360.29011360.22952640X-RAY DIFFRACTION100
3.4936-3.59640.2331360.21412605X-RAY DIFFRACTION100
3.5964-3.71250.24711440.20972652X-RAY DIFFRACTION100
3.7125-3.84520.22151550.19672567X-RAY DIFFRACTION100
3.8452-3.99910.20171270.19052652X-RAY DIFFRACTION100
3.9991-4.18110.22291440.17592633X-RAY DIFFRACTION100
4.1811-4.40150.16481470.15522585X-RAY DIFFRACTION100
4.4015-4.67730.16091650.1442598X-RAY DIFFRACTION100
4.6773-5.03840.17571420.14322650X-RAY DIFFRACTION100
5.0384-5.54530.20091130.15682667X-RAY DIFFRACTION100
5.5453-6.34750.20791170.18762655X-RAY DIFFRACTION100
6.3475-7.99630.21741350.2112662X-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)
13.6880.86280.30882.7779-0.674.80190.3621-0.9789-0.01570.7452-0.3189-0.2173-0.10910.6617-0.04680.5293-0.08370.00750.9427-0.07460.5323-60.276624.265672.4728
28.64193.61555.50475.25434.22619.0242-0.0682-1.56220.2981.1752-0.24720.77310.3782-0.37370.35620.9325-0.18330.24721.3776-0.010.6547-75.512425.262481.4185
32.49581.27050.69365.2722-0.04944.84440.2876-0.70360.1910.4095-0.02660.45530.0756-0.6857-0.24430.3878-0.00880.130.7102-0.01410.5848-74.583221.536759.026
49.24557.59647.26117.76457.26726.88510.14220.197-0.63970.1463-0.219-0.18511.5056-0.9528-0.1721.1102-0.3299-0.06811.1284-0.18090.7601-39.743249.304489.0873
53.5497-0.2554-0.71064.97750.93035.64350.03580.0571-0.38250.0302-0.0038-0.35730.75740.4078-0.03950.50240.1443-0.08820.3918-0.02340.5013-60.832510.281232.2529
63.33320.5059-0.40795.4905-0.03874.8552-0.06080.7517-0.2682-1.46650.0699-0.22520.86640.1010.05911.06540.1632-0.01640.6737-0.17180.6433-60.54838.085311.8733
75.4614-1.5646-0.4014.87042.06892.08870.38610.85320.1459-1.3505-0.39350.0891-0.478-0.08160.13850.91550.22320.03920.74970.05170.726-63.222328.012114.7751
80.9004-0.70872.29694.8661-4.71948.77430.20370.39610.2989-0.4356-0.06020.5213-0.5854-0.2647-0.19050.58690.24470.02730.4827-0.03830.639-69.116732.64124.7209
93.51471.2709-0.98245.09211.40315.7470.2249-0.2153-0.35760.0965-0.1285-0.29390.43920.0771-0.03030.43240.127-0.08890.33780.06550.5287-67.039118.814136.2899
100.62921.30181.20545.70792.27911.7586-0.0978-0.41820.27950.1568-0.1915-0.4455-1.19170.27080.10461.2118-0.2287-0.03280.7218-0.22630.8883-69.287-24.35278.61
118.4419-1.8274-3.85596.46022.00138.079-0.04320.32840.2751-0.06860.17070.2156-0.1761-0.412-0.13540.3388-0.0052-0.06680.29030.0930.4172-2.74248.849711.2257
123.6398-0.68040.25852.74690.27965.0657-0.1972-0.92950.48710.46480.23740.015-0.8193-0.5639-0.04020.6220.22340.06110.6573-0.12890.7076-8.868716.776129.0809
138.71091.3245-3.25749.6372-1.41249.51510.0372-1.5741-0.68210.661-0.1291-0.3036-0.42910.15910.1060.54550.1875-0.05770.88630.03930.6114-0.85163.677337.6112
145.0871-0.1556-0.14465.74110.65632.44380.3497-1.3438-0.91940.84110.6008-1.12780.27011.2873-0.5140.58720.1065-0.15651.1437-0.15120.881911.62264.317529.1439
152.35760.8557-0.13833.1298-1.33055.7044-0.1581-0.158-0.21910.11990.0087-0.17680.33530.51020.15390.36030.08970.01580.362-0.0060.62576.49261.432315.6419
165.8963-2.1943-2.94912.53781.65335.7779-0.10290.46680.18220.14020.14490.2104-0.198-0.52670.11640.32810.1017-0.09350.35440.10260.513-5.87916.86958.9883
176.9862-6.6949-6.39068.31816.41695.8145-0.5368-0.3486-0.14720.0979-0.32880.10470.943-0.46831.01310.7360.2360.24241.458-0.08711.0484-32.927216.021435.5899
184.04723.66592.13917.0756-0.83823.29620.3198-0.25260.67330.1916-0.1377-0.2284-0.58121.0589-0.14430.48590.06660.09310.8097-0.1340.7963-48.460332.167342.2106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 213 through 400 )
2X-RAY DIFFRACTION2chain 'C' and (resid 401 through 478 )
3X-RAY DIFFRACTION3chain 'C' and (resid 479 through 606 )
4X-RAY DIFFRACTION4chain 'C' and (resid 607 through 670 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 283 )
6X-RAY DIFFRACTION6chain 'A' and (resid 284 through 435 )
7X-RAY DIFFRACTION7chain 'A' and (resid 436 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 535 )
9X-RAY DIFFRACTION9chain 'A' and (resid 536 through 606 )
10X-RAY DIFFRACTION10chain 'A' and (resid 607 through 670 )
11X-RAY DIFFRACTION11chain 'B' and (resid 214 through 241 )
12X-RAY DIFFRACTION12chain 'B' and (resid 242 through 410 )
13X-RAY DIFFRACTION13chain 'B' and (resid 411 through 454 )
14X-RAY DIFFRACTION14chain 'B' and (resid 455 through 496 )
15X-RAY DIFFRACTION15chain 'B' and (resid 497 through 567 )
16X-RAY DIFFRACTION16chain 'B' and (resid 568 through 606 )
17X-RAY DIFFRACTION17chain 'B' and (resid 607 through 640 )
18X-RAY DIFFRACTION18chain 'B' and (resid 641 through 670 )

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