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- PDB-1osx: Solution Structure of the Extracellular Domain of BLyS Receptor 3... -

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Basic information

Entry
Database: PDB / ID: 1osx
TitleSolution Structure of the Extracellular Domain of BLyS Receptor 3 (BR3)
ComponentsTumor necrosis factor receptor superfamily member 13C
KeywordsIMMUNE SYSTEM / cysteine-rich domain / extracellular domain / tumor necrosis factor receptor
Function / homology
Function and homology information


B cell costimulation / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of T cell proliferation / positive regulation of B cell proliferation / tumor necrosis factor-mediated signaling pathway / T cell costimulation / TNFR2 non-canonical NF-kB pathway / signaling receptor activity / adaptive immune response / external side of plasma membrane / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 13C, TALL-1 binding domain / Tumour necrosis factor receptor 13C / BAFF-R, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing
AuthorsGordon, N.C. / Pan, B. / Hymowitz, S.G. / Yin, J.P. / Kelley, R.F. / Cochran, A.G. / Yan, M. / Dixit, V.M. / Fairbrother, W.J. / Starovasnik, M.A.
CitationJournal: Biochemistry / Year: 2003
Title: BAFF/BLyS receptor 3 comprises a minimal TNF receptor-like module that encodes a highly focused ligand-binding site
Authors: Gordon, N.C. / Pan, B. / Hymowitz, S.G. / Yin, J.P. / Kelley, R.F. / Cochran, A.G. / Yan, M. / Dixit, V.M. / Fairbrother, W.J. / Starovasnik, M.A.
History
DepositionMar 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)6,5421
Polymers6,5421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 128structures with the lowest restraint violation energy
RepresentativeModel #1lowest restraint violation energy

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 13C / B cell- activating factor receptor / BAFF receptor / BAFF-R / BLyS receptor 3


Mass: 6541.661 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13C OR BAFFR OR BR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RJ3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
141HNHB
1533D (H)CCH-COSY
1633D (H)CCH-TOCSY
1723D HNCO
1823D HNCA
1923D CBCA(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM BR3 U-15N,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d1092%H2O/8%D2O
21.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d1092%H2O/8%D2O
31.5 mM BR3 U-15N,13C,25 mM Na2PO4, 50 mM NaCl, 0.1 mM NaN3, 0.1 mM DSS-d10100% D2O
Sample conditionsIonic strength: 50 mM NaCl, 25 mM Na2PO4 / pH: 5.0 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Brukercollection
Felix98Accelrysdata analysis
X-PLOR98Accelrysstructure solution
X-PLOR98Brungerrefinement
RefinementMethod: torsion angle dynamics simulated annealing / Software ordinal: 1
Details: Only 19 residues, including Cys19 through Leu37 are ordered in solution, while the rest of the extracellular domain is highly flexible (based on 1H-15N heteronuclear NOE analysis). ...Details: Only 19 residues, including Cys19 through Leu37 are ordered in solution, while the rest of the extracellular domain is highly flexible (based on 1H-15N heteronuclear NOE analysis). Furthermore, the BAFF-binding domain of BR3 was found to reside within a fragment consisting of Thr17-Arg42 denoted miniBR3. Thus, the structure of BR3 was calculated only for these 26 residues, based on a total of 315 distance and 46 dihedral angle restraints derived from analysis of NMR data colleected on the entire BR3 ECD.
NMR representativeSelection criteria: lowest restraint violation energy
NMR ensembleConformer selection criteria: structures with the lowest restraint violation energy
Conformers calculated total number: 128 / Conformers submitted total number: 20

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