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- PDB-6ool: Structural elucidation of the Ectodomain of mouse UNC5H2 -

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Basic information

Entry
Database: PDB / ID: 6ool
TitleStructural elucidation of the Ectodomain of mouse UNC5H2
ComponentsNetrin receptor UNC5B
KeywordsPROTEIN BINDING / cell signaling / netrin / dependence receptor / apoptosis
Function / homology
Function and homology information


netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process ...netrin receptor activity / anterior/posterior axon guidance / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / axon guidance / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process / plasma membrane / cytosol
Similarity search - Function
UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type 1 domain / Death domain profile. ...UNC5B, death domain / UPA domain / Netrin receptor UNC5 / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Thrombospondin type 1 domain / Death domain profile. / 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 UNC5B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStetefeld, J. / McDougall, M.D. / Loewen, P.C. / Moya, A. / Meier, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-152935 Canada
CitationJournal: To be published
Title: Structural elucidation of the Ectodomain of mouse UNC5H2
Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C. / Moya, A. / Meier, M.
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Netrin receptor UNC5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,53817
Polymers39,1461
Non-polymers1,39216
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.051, 76.890, 159.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Netrin receptor UNC5B / Protein unc-5 homolog 2 / Protein unc-5 homolog B


Mass: 39145.793 Da / Num. of mol.: 1 / Fragment: unc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Unc5b, Unc5h2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8K1S3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / 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
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 4.6 mg/ml UNC5HC, 100 mM HEPES, 3M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 16, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→159.01 Å / Num. all: 17631 / Num. obs: 17631 / % possible obs: 100 % / Redundancy: 6.3 % / Rpim(I) all: 0.068 / Rrim(I) all: 0.172 / Rsym value: 0.157 / Net I/av σ(I): 3.9 / Net I/σ(I): 7.7 / Num. measured all: 111360
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.956.40.71.11630425320.30.7620.72.3100
2.95-3.136.50.4091.81536223750.1750.4450.4093.7100
3.13-3.356.50.292.41455322510.1240.3160.294.8100
3.35-3.616.30.2332.81330020980.1010.2540.2336.3100
3.61-3.966.10.1893.21185019480.0840.2070.1899.1100
3.96-4.436.30.0986.41124217800.0420.1070.09811.3100
4.43-5.116.30.1214.71006015870.0520.1320.12112.4100
5.11-6.266.30.1015.8848513450.0430.110.10111.9100
6.26-8.856.20.0688.6663710760.030.0740.06812.8100
8.85-79.5055.60.0571135676390.0260.0620.05714.999

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FFT

5fft


Resolution: 2.8→39.78 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.203 / SU ML: 0.22 / SU R Cruickshank DPI: 0.3182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.272 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 903 5.2 %RANDOM
Rwork0.2198 ---
obs0.2222 16578 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.21 Å2 / Biso mean: 54.872 Å2 / Biso min: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--6.43 Å20 Å2
3----5.75 Å2
Refinement stepCycle: final / Resolution: 2.8→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 73 55 2086
Biso mean--100.13 43.52 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132103
X-RAY DIFFRACTIONr_bond_other_d0.0040.0171873
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.6922872
X-RAY DIFFRACTIONr_angle_other_deg1.3991.6134359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6975248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.921.721122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48615334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6471518
X-RAY DIFFRACTIONr_chiral_restr0.1220.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 62 -
Rwork0.402 1203 -
all-1265 -
obs--100 %

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