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- PDB-3g5b: The structure of UNC5b cytoplasmic domain -

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Basic information

Entry
Database: PDB / ID: 3g5b
TitleThe structure of UNC5b cytoplasmic domain
ComponentsNetrin receptor UNC5B
KeywordsAPOPTOSIS / ZU5 / Death domain / UPA / Developmental protein / Glycoprotein / Immunoglobulin domain / Membrane / Phosphoprotein / Receptor / Transmembrane
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 / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / apoptotic process / plasma membrane
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
PHOSPHATE ION / Netrin receptor UNC5B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsWang, R. / Wei, Z. / Zhang, M.
CitationJournal: Mol.Cell / Year: 2009
Title: Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor
Authors: Wang, R. / Wei, Z. / Jin, H. / Wu, H. / Yu, C. / Wen, W. / Chan, L.-N. / Wen, Z. / Zhang, M.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Netrin receptor UNC5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8724
Polymers44,5871
Non-polymers2853
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.243, 62.710, 118.110
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 B / Unc-5 homolog 2


Mass: 44586.750 Da / Num. of mol.: 1 / Fragment: UNP residues 541-945 / Mutation: S542G, T744P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc5b / Plasmid: modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O08722
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.4~0.5M Ammonium Phosphate, 0.1M MES Buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2007
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 25672 / Num. obs: 25672 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074
Reflection shellResolution: 2→2.11 Å / Redundancy: 6 % / Rmerge(I) obs: 0.381 / Num. unique all: 3572 / Rsym value: 0.381 / % possible all: 95.8

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RESOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2→27.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.206 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1293 5.1 %RANDOM
Rwork0.193 ---
obs0.196 25576 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.07 Å2 / Biso mean: 36.747 Å2 / Biso min: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2--0.83 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 2→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 15 226 3232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223076
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9774195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64824125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9115515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3571516
X-RAY DIFFRACTIONr_chiral_restr0.0740.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022288
X-RAY DIFFRACTIONr_nbd_refined0.190.21312
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.219
X-RAY DIFFRACTIONr_mcbond_it1.9821989
X-RAY DIFFRACTIONr_mcangle_it3.03333109
X-RAY DIFFRACTIONr_scbond_it3.93241245
X-RAY DIFFRACTIONr_scangle_it5.54661080
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 108 -
Rwork0.234 1666 -
all-1774 -
obs--94.61 %

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