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- PDB-7zav: GPC3-Unc5D octamer structure and role in cell migration -

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Basic information

Entry
Database: PDB / ID: 7zav
TitleGPC3-Unc5D octamer structure and role in cell migration
ComponentsGlypican-3
KeywordsSIGNALING PROTEIN / Glycoprotein / Migration
Function / homology
Function and homology information


Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / HS-GAG degradation / peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / regulation of non-canonical Wnt signaling pathway / Retinoid metabolism and transport / mesenchymal cell proliferation involved in ureteric bud development ...Glycosaminoglycan-protein linkage region biosynthesis / HS-GAG biosynthesis / HS-GAG degradation / peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / regulation of non-canonical Wnt signaling pathway / Retinoid metabolism and transport / mesenchymal cell proliferation involved in ureteric bud development / cell proliferation involved in metanephros development / cell migration involved in gastrulation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / negative regulation of growth / positive regulation of Wnt signaling pathway, planar cell polarity pathway / positive regulation of BMP signaling pathway / coronary vasculature development / positive regulation of smoothened signaling pathway / regulation of growth / embryonic hindlimb morphogenesis / regulation of canonical Wnt signaling pathway / anterior/posterior axis specification / Wnt signaling pathway, planar cell polarity pathway / branching involved in ureteric bud morphogenesis / smoothened signaling pathway / bone mineralization / positive regulation of endocytosis / canonical Wnt signaling pathway / side of membrane / lung development / osteoclast differentiation / animal organ morphogenesis / epithelial cell proliferation / positive regulation of D-glucose import / negative regulation of smoothened signaling pathway / response to bacterium / kidney development / negative regulation of canonical Wnt signaling pathway / Golgi lumen / negative regulation of epithelial cell proliferation / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / lysosome / negative regulation of cell population proliferation / plasma membrane
Similarity search - Function
Glypican, conserved site / Glypicans signature. / Glypican / Glypican
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAkkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Ritu, R. / Agirre, J. ...Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Ritu, R. / Agirre, J. / Aksu, M. / White, E. / Lowe, E. / Ben Amar, D. / Zaballa, S. / Huo, J. / Pakos, I. / McCubbin, P. / Comoletti, D. / Owens, R. / Robinson, C. / Castellani, V. / del Toro, D. / Seiradake, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202827/Z/16/Z United Kingdom
Citation
Journal: Cell / Year: 2022
Title: GPC3-Unc5 receptor complex structure and role in cell migration.
Authors: Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero-Ordaz, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Raj, R. / Agirre, J. / Aksu, M. / White, E.S. ...Authors: Akkermans, O. / Delloye-Bourgeois, C. / Peregrina, C. / Carrasquero-Ordaz, M. / Kokolaki, M. / Berbeira-Santana, M. / Chavent, M. / Reynaud, F. / Raj, R. / Agirre, J. / Aksu, M. / White, E.S. / Lowe, E. / Ben Amar, D. / Zaballa, S. / Huo, J. / Pakos, I. / McCubbin, P.T.N. / Comoletti, D. / Owens, R.J. / Robinson, C.V. / Castellani, V. / Del Toro, D. / Seiradake, E.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glypican-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7663
Polymers53,3241
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint6 kcal/mol
Surface area17730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.488, 100.488, 90.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Glypican-3


Mass: 53323.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpc3 / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q8CFZ4
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate and 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.9→90.76 Å / Num. obs: 12106 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 92.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.065 / Rrim(I) all: 0.143 / Net I/σ(I): 9.2
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 875 / CC1/2: 0.493 / Rpim(I) all: 0.999 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWT

4ywt


Resolution: 2.9→43.94 Å / SU ML: 0.2961 / Cross valid method: FREE R-VALUE / Phase error: 31.8973
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 569 4.71 %
Rwork0.2183 11502 -
obs0.2203 12081 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.61 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 28 0 2786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362834
X-RAY DIFFRACTIONf_angle_d0.66223832
X-RAY DIFFRACTIONf_chiral_restr0.0414449
X-RAY DIFFRACTIONf_plane_restr0.0045483
X-RAY DIFFRACTIONf_dihedral_angle_d4.3275387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.190.37641480.32752777X-RAY DIFFRACTION98.88
3.19-3.650.33691070.26232889X-RAY DIFFRACTION100
3.65-4.60.27011540.2242863X-RAY DIFFRACTION99.97
4.6-43.940.22831600.18582973X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -18.4804829562 Å / Origin y: -24.6206763277 Å / Origin z: 12.1716553409 Å
111213212223313233
T0.577224364911 Å20.0633586385083 Å2-0.0612280990188 Å2-0.564854843509 Å2-0.000908937050743 Å2--0.537768595726 Å2
L1.16948545859 °2-1.53069843063 °20.575853042985 °2-2.21611116178 °2-0.986875068224 °2--0.302936461396 °2
S-0.0832669117778 Å °-0.247563771081 Å °-0.0693286784865 Å °0.0900906837871 Å °0.158491773555 Å °0.156724452332 Å °-0.0547193865458 Å °-0.16364222287 Å °0.000123750621058 Å °
Refinement TLS groupSelection details: all

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