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- PDB-7za1: GPC3-Unc5D octamer structure and role in cell migration -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7za1
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


peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / regulation of protein localization to membrane / netrin receptor activity / 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 ...peptidyl-dipeptidase inhibitor activity / mesonephric duct morphogenesis / body morphogenesis / cell proliferation involved in kidney development / regulation of protein localization to membrane / netrin receptor activity / 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 / cell-cell adhesion via plasma-membrane adhesion molecules / regulation of neuron migration / coronary vasculature development / pyramidal neuron differentiation / positive regulation of BMP signaling pathway / 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 / negative regulation of smoothened signaling pathway / lysosomal lumen / osteoclast differentiation / epithelial cell proliferation / axon guidance / positive regulation of D-glucose import / 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 / collagen-containing extracellular matrix / Attachment and Entry / endoplasmic reticulum lumen / apoptotic process / cell surface / plasma membrane
Similarity search - Function
UNC5D, Death domain / Glypican, conserved site / Glypicans signature. / UPA domain / Netrin receptor UNC5 / UPA domain / Glypican / Glypican / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain ...UNC5D, Death domain / Glypican, conserved site / Glypicans signature. / UPA domain / Netrin receptor UNC5 / UPA domain / 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 speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)341,72131
Polymers334,5678
Non-polymers7,15523
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)102.643, 157.584, 126.601
Angle α, β, γ (deg.)90.000, 102.949, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules EFGHACDB

#1: 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
#2: Protein
Glypican-3 / GTR2-2 / Intestinal protein OCI-5 / MXR7


Mass: 53383.656 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPC3, OCI5 / Plasmid: pHL-sec / Cell line (production host): HEK293S GnTi- / Production host: Homo sapiens (human) / References: UniProt: P51654

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Sugars , 4 types, 23 molecules

#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 12 / 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
#6: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6 / 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

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Details

Has ligand of interestN

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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: 58.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / 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: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 4.1→123.4 Å / Num. obs: 22459 / % possible obs: 73 % / Redundancy: 3.4 % / Biso Wilson estimate: 143.4 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.071 / Rrim(I) all: 0.13 / Net I/σ(I): 3.4
Reflection shellResolution: 4.1→4.55 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 900 / CC1/2: 0.738 / % possible all: 10.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FTT, hGPC3

5ftt


Resolution: 4.1→97.336 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.831 / SU B: 363.618 / SU ML: 2.062 / Cross valid method: FREE R-VALUE / ESU R Free: 1.915
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3648 899 4.886 %
Rwork0.3239 17500 -
all0.326 --
obs-18399 59.546 %
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: 186.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.883 Å2-0 Å21.725 Å2
2--3.2 Å20 Å2
3----4.41 Å2
Refinement stepCycle: LAST / Resolution: 4.1→97.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19184 0 462 0 19646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01320100
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518879
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.67427248
X-RAY DIFFRACTIONr_angle_other_deg1.5561.60543546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.23352384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77622.5141058
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.034153496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.08415132
X-RAY DIFFRACTIONr_chiral_restr0.0790.22693
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222295
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024633
X-RAY DIFFRACTIONr_nbd_refined0.2350.24260
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.218176
X-RAY DIFFRACTIONr_nbtor_refined0.1730.29607
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.211079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3450.219
X-RAY DIFFRACTIONr_nbd_other0.3090.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.21
X-RAY DIFFRACTIONr_mcbond_it3.64311.7579608
X-RAY DIFFRACTIONr_mcbond_other3.64211.7579607
X-RAY DIFFRACTIONr_mcangle_it6.56217.62811968
X-RAY DIFFRACTIONr_mcangle_other6.56217.62811969
X-RAY DIFFRACTIONr_scbond_it2.88212.04210492
X-RAY DIFFRACTIONr_scbond_other2.88212.04210493
X-RAY DIFFRACTIONr_scangle_it5.45717.95915280
X-RAY DIFFRACTIONr_scangle_other5.45717.95915281
X-RAY DIFFRACTIONr_lrange_it17.238220.41979345
X-RAY DIFFRACTIONr_lrange_other17.238220.41879346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.2070.507140.412196X-RAY DIFFRACTION9.3292
4.207-4.3220.48160.403212X-RAY DIFFRACTION10.2656
4.322-4.4470.39180.36248X-RAY DIFFRACTION12.3721
4.447-4.5830.407190.356344X-RAY DIFFRACTION17.3352
4.583-4.7340.339260.333458X-RAY DIFFRACTION23.7371
4.734-4.8990.399300.349629X-RAY DIFFRACTION33.4179
4.899-5.0840.44490.353853X-RAY DIFFRACTION47.5989
5.084-5.2910.378470.3551157X-RAY DIFFRACTION66.2631
5.291-5.5260.359750.3621394X-RAY DIFFRACTION83.8949
5.526-5.7950.415740.381549X-RAY DIFFRACTION96.78
5.795-6.1080.408610.3991526X-RAY DIFFRACTION99.6234
6.108-6.4780.455690.3681445X-RAY DIFFRACTION100
6.478-6.9230.392650.3931355X-RAY DIFFRACTION100
6.923-7.4760.445620.3391271X-RAY DIFFRACTION100
7.476-8.1870.368670.291141X-RAY DIFFRACTION99.8347
8.187-9.1480.28520.251060X-RAY DIFFRACTION99.9101
9.148-10.5540.279590.228922X-RAY DIFFRACTION99.5939
10.554-12.9020.268360.234785X-RAY DIFFRACTION98.5594
12.902-18.1470.308360.321607X-RAY DIFFRACTION98.318
18.147-97.3360.514240.479348X-RAY DIFFRACTION98.6737
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)
10.2056-0.1203-1.16750.81810.85377.9950.2066-0.0083-0.0190.07820.0032-0.0877-0.9274-0.2483-0.20980.60560.0835-0.03810.57930.04280.54641.338223.211633.5382
21.25980.00920.72713.38152.02387.5509-0.4593-0.5080.16580.75360.35340.4314-0.03680.28360.1060.48980.0194-0.17970.76220.00851.317727.907354.014929.4676
30.3091-0.2956-1.41911.3641.09338.1982-0.09810.0744-0.1502-0.0756-0.05690.09480.5724-0.42780.15490.455-0.1086-0.05480.5799-0.00450.70968.404743.1046-2.8895
40.7051-0.4789-1.25012.39472.29385.10290.04880.1791-0.0114-0.0638-0.051-0.110.0763-0.08130.00230.45110.0333-0.34070.64170.05731.01533.523115.191912.4502
57.30934.85470.01246.7378-1.41621.57870.4425-0.4130.09730.3859-0.36560.0236-0.6111-0.3127-0.07680.5280.3184-0.07460.2737-0.0880.1117-4.493457.30834.029
66.8872-3.54664.04565.3615-2.58975.08470.44410.4945-0.4727-0.8794-0.0920.3383-0.30340.4121-0.35210.481-0.2170.05450.2874-0.27560.654641.067942.3342-8.6196
75.84832.5109-1.06065.0303-0.19342.46080.3947-0.67230.55580.69170.09860.72330.51280.5357-0.49330.99510.2177-0.49120.9305-0.07370.843429.412327.702852.0764
87.3874-4.08193.4615.9036-3.02743.98690.15060.1275-0.1049-0.3714-0.3365-0.07320.6311-0.12760.1860.3398-0.07190.15030.1113-0.14810.33086.42578.5373-4.8414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLE51 - 301
2X-RAY DIFFRACTION1ALLE302
3X-RAY DIFFRACTION1ALLE303
4X-RAY DIFFRACTION1ALLE304
5X-RAY DIFFRACTION2ALLF51 - 301
6X-RAY DIFFRACTION2ALLF302
7X-RAY DIFFRACTION2ALLF304
8X-RAY DIFFRACTION2ALLF305
9X-RAY DIFFRACTION3ALLG51 - 301
10X-RAY DIFFRACTION3ALLG302
11X-RAY DIFFRACTION4ALLH51 - 301
12X-RAY DIFFRACTION4ALLH302
13X-RAY DIFFRACTION4ALLH303
14X-RAY DIFFRACTION4ALLH304
15X-RAY DIFFRACTION5ALLA62 - 477
16X-RAY DIFFRACTION5ALLA478
17X-RAY DIFFRACTION5ALLA479
18X-RAY DIFFRACTION5ALLA480
19X-RAY DIFFRACTION5ALLA481
20X-RAY DIFFRACTION5ALLA482
21X-RAY DIFFRACTION6ALLC62 - 477
22X-RAY DIFFRACTION6ALLC478
23X-RAY DIFFRACTION6ALLC479
24X-RAY DIFFRACTION6ALLC481
25X-RAY DIFFRACTION6ALLC482
26X-RAY DIFFRACTION7ALLD62 - 477
27X-RAY DIFFRACTION7ALLD478
28X-RAY DIFFRACTION7ALLD479
29X-RAY DIFFRACTION7ALLD480
30X-RAY DIFFRACTION7ALLD483
31X-RAY DIFFRACTION8ALLB62 - 477
32X-RAY DIFFRACTION8ALLB478
33X-RAY DIFFRACTION8ALLB479
34X-RAY DIFFRACTION8ALLB480
35X-RAY DIFFRACTION8ALLB481
36X-RAY DIFFRACTION8ALLB482

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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