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- PDB-7za2: GPC3-Unc5D octamer structure and role in cell migration -

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Basic information

Entry
Database: PDB / ID: 7za2
TitleGPC3-Unc5D octamer structure and role in cell migration
Components
  • Glypican-3
  • Netrin receptor UNC5D
KeywordsSIGNALING PROTEIN / Complex / Cell migration / Glycan-Glycan Interaction
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 / netrin receptor activity / regulation of non-canonical Wnt signaling pathway / Retinoid metabolism and transport ...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 / netrin receptor activity / 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 / regulation of neuron migration / positive regulation of smoothened signaling pathway / regulation of growth / embryonic hindlimb morphogenesis / regulation of canonical Wnt signaling pathway / pyramidal neuron differentiation / 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 / axon guidance / 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 / apoptotic process / cell surface / plasma membrane
Similarity search - Function
UNC5D, Death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Glypican, conserved site / Glypicans signature. / Glypican / Glypican / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain ...UNC5D, Death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Glypican, conserved site / Glypicans signature. / Glypican / Glypican / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-D-mannopyranose / Netrin receptor UNC5D / Glypican-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 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 21, 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Glypican-3
B: Glypican-3
C: Glypican-3
D: Glypican-3
E: Netrin receptor UNC5D
F: Netrin receptor UNC5D
G: Netrin receptor UNC5D
H: Netrin receptor UNC5D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,38826
Polymers334,3268
Non-polymers4,06218
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Native Mass spectrometry Molecular dynamics Mutational analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.113, 157.994, 126.572
Angle α, β, γ (deg.)90.000, 102.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glypican-3


Mass: 53323.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gpc3 / Plasmid: pHL-sec / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q8CFZ4
#2: Protein
Netrin receptor UNC5D / Protein unc-5 homolog D


Mass: 30257.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc5d / Plasmid: pHl-sec / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: F1LW30
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 14 / 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
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8.5
Details: 15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine ...Details: 15% w/v PEG 3000, 20% v/v 1, 2, 4-butanetrol, 1% w/v NDSB 256, 0.1 M Gly-GLy/AMPD (pH 8.5) and 0.2 M of amino acids (DL-arginine HCL, DL-threonine, DL-histidine HCL H2O, DL-5-hydroxylysine HCL, trans-4-hydroxyl-L-proline).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.6→66.62 Å / Num. obs: 21870 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 245.99 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09281 / Rpim(I) all: 0.03962 / Net I/σ(I): 7.77
Reflection shellResolution: 4.6→4.76 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 2165 / CC1/2: 0.485

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTT, GPC3

5ftt


Resolution: 4.6→66.616 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.891 / SU B: 486.107 / SU ML: 2.381 / Cross valid method: FREE R-VALUE / ESU R Free: 1.626
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.347 1866 8.555 %
Rwork0.3075 19946 -
all0.311 --
obs-21812 99.621 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 331.565 Å2
Baniso -1Baniso -2Baniso -3
1-15.254 Å2-0 Å29.105 Å2
2---7.738 Å2-0 Å2
3----10.578 Å2
Refinement stepCycle: LAST / Resolution: 4.6→66.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19188 0 257 0 19445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01319883
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518735
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.65826919
X-RAY DIFFRACTIONr_angle_other_deg1.5211.59343163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7452384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36122.5281060
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.498153504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.21215132
X-RAY DIFFRACTIONr_chiral_restr0.0690.22609
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024630
X-RAY DIFFRACTIONr_nbd_refined0.2280.24148
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.218138
X-RAY DIFFRACTIONr_nbtor_refined0.1730.29399
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.211340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1380.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3250.228
X-RAY DIFFRACTIONr_nbd_other0.3120.275
X-RAY DIFFRACTIONr_mcbond_it9.70321.1839608
X-RAY DIFFRACTIONr_mcbond_other9.70121.1829607
X-RAY DIFFRACTIONr_mcangle_it16.7531.75411968
X-RAY DIFFRACTIONr_mcangle_other16.74931.75511969
X-RAY DIFFRACTIONr_scbond_it8.30821.99910275
X-RAY DIFFRACTIONr_scbond_other8.30721.99910276
X-RAY DIFFRACTIONr_scangle_it15.20732.70114951
X-RAY DIFFRACTIONr_scangle_other15.20732.70114952
X-RAY DIFFRACTIONr_lrange_it34.816398.59579008
X-RAY DIFFRACTIONr_lrange_other34.816398.59279009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-4.7190.4711370.4411461X-RAY DIFFRACTION99.5639
4.719-4.8480.4051360.4031423X-RAY DIFFRACTION100
4.848-4.9880.4141270.3631391X-RAY DIFFRACTION99.8028
4.988-5.1420.3371260.341363X-RAY DIFFRACTION99.5987
5.142-5.310.371220.3151305X-RAY DIFFRACTION99.7205
5.31-5.4960.3761180.3091267X-RAY DIFFRACTION100
5.496-5.7030.4171170.3431230X-RAY DIFFRACTION99.6302
5.703-5.9350.3971070.3491183X-RAY DIFFRACTION99.9225
5.935-6.1990.4631070.3781115X-RAY DIFFRACTION100
6.199-6.50.4861020.3811100X-RAY DIFFRACTION99.9169
6.5-6.8510.388970.3441038X-RAY DIFFRACTION99.912
6.851-7.2650.383910.309974X-RAY DIFFRACTION99.9062
7.265-7.7650.314860.256911X-RAY DIFFRACTION100
7.765-8.3840.296810.233858X-RAY DIFFRACTION99.7875
8.384-9.180.287740.221794X-RAY DIFFRACTION99.8849
9.18-10.2570.306680.207721X-RAY DIFFRACTION99.4956
10.257-11.830.276570.226629X-RAY DIFFRACTION98.4218
11.83-14.4550.274510.254537X-RAY DIFFRACTION99.1568
14.455-20.3040.409400.385412X-RAY DIFFRACTION98.69
20.304-66.6160.365220.55234X-RAY DIFFRACTION94.4649
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)
18.28845.41080.20028.6917-0.532.9450.5107-0.72720.18960.3915-0.65780.1447-0.669-0.26520.14720.76510.4577-0.24660.9983-0.16930.1015-5.194457.330134.4173
26.66740.339-2.0657.65250.23084.82570.6773-1.09690.62750.97030.170.93750.30470.813-0.84731.424-0.1056-0.47832.6711-0.03860.561729.248128.120652.4795
38.5519-4.29523.25637.8138-3.21035.91110.53340.43860.1386-0.9328-0.87-0.13580.51240.11630.33660.22780.1411-0.13990.8052-0.33040.36326.10068.8088-4.303
46.9405-3.84055.16986.2797-3.4976.93230.57650.46270.0125-1.0389-0.14010.4505-0.54460.487-0.43640.7143-0.1631-0.03881.5688-0.1510.798341.074842.6715-7.8919
50.3006-0.2808-1.6251.5372.373313.42830.1891-0.0141-0.08090.0606-0.14650.0695-1.395-0.6115-0.04261.0730.1154-0.12841.52430.04950.78221.363323.890134.3993
61.752-1.3061-0.9264.35142.88978.24260.0855-0.60850.53140.94630.24520.03220.1608-0.255-0.33060.8067-0.2218-0.18512.0558-0.1181.694927.302354.47229.9762
71.6716-0.7-3.58081.82371.066610.7955-0.24250.5543-0.1085-0.3840.0583-0.18991.5252-0.94460.18421.5566-0.36070.05571.84590.00180.4738.329943.1499-2.5151
81.481-1.1304-2.48643.3633.29627.77770.25740.12940.0544-0.1579-0.0671-0.25410.22760.0624-0.19030.7097-0.0741-0.42741.58770.05081.500633.500615.711213.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA61 - 476
2X-RAY DIFFRACTION2ALLB61 - 476
3X-RAY DIFFRACTION2ALLB477
4X-RAY DIFFRACTION3ALLC61 - 476
5X-RAY DIFFRACTION3ALLC477
6X-RAY DIFFRACTION4ALLD61 - 476
7X-RAY DIFFRACTION4ALLD477
8X-RAY DIFFRACTION5ALLE51 - 301
9X-RAY DIFFRACTION5ALLE303
10X-RAY DIFFRACTION5ALLE304
11X-RAY DIFFRACTION6ALLF51 - 301
12X-RAY DIFFRACTION6ALLF302
13X-RAY DIFFRACTION6ALLF303
14X-RAY DIFFRACTION7ALLG51 - 301
15X-RAY DIFFRACTION7ALLG302
16X-RAY DIFFRACTION7ALLG303
17X-RAY DIFFRACTION8ALLH51 - 301
18X-RAY DIFFRACTION8ALLH302
19X-RAY DIFFRACTION8ALLH303

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