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

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Basic information

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


peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / regulation of protein localization to membrane / body morphogenesis / cell proliferation involved in kidney development / regulation of non-canonical Wnt signaling pathway / mesenchymal cell proliferation involved in ureteric bud development / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD ...peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / regulation of protein localization to membrane / body morphogenesis / cell proliferation involved in kidney development / regulation of non-canonical Wnt signaling pathway / mesenchymal cell proliferation involved in ureteric bud development / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / cell proliferation involved in metanephros development / A tetrasaccharide linker sequence is required for GAG synthesis / cell migration involved in gastrulation / HS-GAG biosynthesis / HS-GAG degradation / 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 / 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 / RSV-host interactions / positive regulation of endocytosis / Respiratory syncytial virus (RSV) attachment and entry / anatomical structure morphogenesis / canonical Wnt signaling pathway / Retinoid metabolism and transport / side of membrane / osteoclast differentiation / lysosomal lumen / epithelial cell proliferation / positive regulation of D-glucose import / negative regulation of smoothened signaling pathway / Post-translational protein phosphorylation / response to bacterium / lung development / negative regulation of canonical Wnt signaling pathway / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of protein catabolic process / negative regulation of epithelial cell proliferation / positive regulation of canonical Wnt signaling pathway / cell migration / : / Attachment and Entry / endoplasmic reticulum lumen / cell surface / plasma membrane
Similarity search - Function
Glypican, conserved site / Glypicans signature. / Glypican / Glypican
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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)53,8263
Polymers53,3841
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.190, 100.190, 90.186
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 / GTR2-2 / Intestinal protein OCI-5 / MXR7


Mass: 53383.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPC3, OCI5 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P51654
#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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris/BICINE (pH 8.5) and 0.02 M of amino acids (L-Na-glutamate, alanine, glycine, lysine-HCl, and serine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.58→86.86 Å / Num. obs: 16895 / % possible obs: 100 % / Redundancy: 15.5 % / Biso Wilson estimate: 87.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Rrim(I) all: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1239 / CC1/2: 0.324 / Rpim(I) all: 1.39 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWT

4ywt


Resolution: 2.58→50.09 Å / SU ML: 0.5552 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.5576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2849 818 4.85 %
Rwork0.2302 16042 -
obs0.2329 16860 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.43 Å2
Refinement stepCycle: LAST / Resolution: 2.58→50.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 28 0 2864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352912
X-RAY DIFFRACTIONf_angle_d0.67883933
X-RAY DIFFRACTIONf_chiral_restr0.0405458
X-RAY DIFFRACTIONf_plane_restr0.0046497
X-RAY DIFFRACTIONf_dihedral_angle_d4.6435394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.740.37551220.35622612X-RAY DIFFRACTION98.99
2.74-2.950.44861540.3572625X-RAY DIFFRACTION99.89
2.95-3.250.38091150.31532660X-RAY DIFFRACTION99.96
3.25-3.720.35351430.27012659X-RAY DIFFRACTION99.93
3.72-4.680.25551330.21312696X-RAY DIFFRACTION100
4.68-50.090.24451510.19472790X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -19.0789262058 Å / Origin y: -23.9386677376 Å / Origin z: 11.8014785731 Å
111213212223313233
T0.818257475334 Å20.0615209378506 Å2-0.039922496047 Å2-0.83969118456 Å2-0.00248050472335 Å2--0.591832218749 Å2
L3.26197361155 °2-3.990197851 °21.3850225706 °2-5.23242240651 °2-1.93121244437 °2--0.726101189782 °2
S-0.333783836443 Å °-0.377385236967 Å °-0.0497013788211 Å °0.371115289397 Å °0.40926492713 Å °0.215633045534 Å °-0.186824814298 Å °-0.178554187641 Å °-0.0704988733664 Å °
Refinement TLS groupSelection details: all

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