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- PDB-1xut: Solution structure of TACI-CRD2 -

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Basic information

Entry
Database: PDB / ID: 1xut
TitleSolution structure of TACI-CRD2
ComponentsTumor necrosis factor receptor superfamily member 13B
KeywordsCYTOKINE Receptor / TNF Receptor / cytokine / cysteine-rich domain / receptor
Function / homology
Function and homology information


TNFs bind their physiological receptors / negative regulation of B cell proliferation / B cell homeostasis / hematopoietic progenitor cell differentiation / signaling receptor activity / adaptive immune response / cell surface receptor signaling pathway / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor fold / Tumor necrosis factor receptor superfamily / TACI, cysteine-rich domain / Tumour necrosis factor receptor 13B / TACI, cysteine-rich domain / TNFR/NGFR family cysteine-rich region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / THE FINAL STRUCTURES WERE CALCULATED USING THE PROGRAM CNX (VERSION 2002; ACCELRYS, SAN DIEGO, CA).
AuthorsHymowitz, S.G. / Patel, D.R. / Wallweber, H.J. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. ...Hymowitz, S.G. / Patel, D.R. / Wallweber, H.J. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. / Kelley, R.F. / Starovasnik, M.A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structures of APRIL-receptor complexes: like BCMA, TACI employs only a single cysteine-rich domain for high affinity ligand binding.
Authors: Hymowitz, S.G. / Patel, D.R. / Wallweber, H.J. / Runyon, S. / Yan, M. / Yin, J. / Shriver, S.K. / Gordon, N.C. / Pan, B. / Skelton, N.J. / Kelley, R.F. / Starovasnik, M.A.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,3171
Polymers5,3171
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 / 100structures with the least restraint violations
RepresentativeModel #1

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Components

#1: Protein/peptide Tumor necrosis factor receptor superfamily member 13B / Transmembrane activator and CAML interactor / TNFRSF13B


Mass: 5317.140 Da / Num. of mol.: 1 / Fragment: TACI_D2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF13B, TACI / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14836
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C-SEPARATED NOESY
1312D NOESY
1413D HNHB
NMR detailsText: ALL NMR DATA WERE PROCESSED USING FELIX (VERSION 2000.1; ACCELRYS, SAN DIEGO, CA) AND ANALYZED USING SPARKY (VERSION 3.11; GODDARD & KNELLER, UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, CA). NOE ...Text: ALL NMR DATA WERE PROCESSED USING FELIX (VERSION 2000.1; ACCELRYS, SAN DIEGO, CA) AND ANALYZED USING SPARKY (VERSION 3.11; GODDARD & KNELLER, UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, CA). NOE ASSIGNMENTS WERE OBTAINED USING CANDID (HERRMANN ET AL., 2002). LOOSE BACKBONE DIGHEDRAL ANGLE RESTRAINTS WERE OBTAINED FROM ANALYSIS OF BACKBONE CHEMICAL SHIFTS WITH THE PROGRAM TALOS (CORNILESCU ET AL., 1999).

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Sample preparation

DetailsContents: 0.8-1.0 MM TACI_D2 UNIFORMLY ENRICHED WITH 15N & 13C, 50 MM SODIUM PHOSPHATE, 150 MM SODIUM CHLORIDE, 1 MM SODIUM AZIDE,DIOXANE, 10% DEUTERIUM OXIDE; 0.8-1.0 MM TACI_D2 UNIFORMLY ENRICHED ...Contents: 0.8-1.0 MM TACI_D2 UNIFORMLY ENRICHED WITH 15N & 13C, 50 MM SODIUM PHOSPHATE, 150 MM SODIUM CHLORIDE, 1 MM SODIUM AZIDE,DIOXANE, 10% DEUTERIUM OXIDE; 0.8-1.0 MM TACI_D2 UNIFORMLY ENRICHED WITH 15N & 13C, 50 MM SODIUM PHOSPHATE, 150 MM SODIUM CHLORIDE, 1 MM SODIUM AZIDE,DIOXANE, 10% DEUTERIUM OXIDE
Sample conditionsIonic strength: 200 mM / pH: 7.2 / Pressure: AMBIENT / Temperature: 290 K

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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
TALOS2002CORNILESCU ET AL, 1999refinement
CNX2002ACCELRYS, SAN DIEGO, CArefinement
Felix2000.1structure solution
Sparky3.11structure solution
XwinNMR3.5structure solution
CYANA1.1structure solution
RefinementMethod: THE FINAL STRUCTURES WERE CALCULATED USING THE PROGRAM CNX (VERSION 2002; ACCELRYS, SAN DIEGO, CA).
Software ordinal: 1
Details: 100 STRUCTURES WERE CALCULATED USING TORSION ANGLE DYNAMICS FOLLOWED BY CARTESION DYNAMICS AND MINIMIZATION. THE 20 STRUCTURES WITH THE LOWEST RESTRAINT VIOLATION ENERGY WERE CHOSEN TO ...Details: 100 STRUCTURES WERE CALCULATED USING TORSION ANGLE DYNAMICS FOLLOWED BY CARTESION DYNAMICS AND MINIMIZATION. THE 20 STRUCTURES WITH THE LOWEST RESTRAINT VIOLATION ENERGY WERE CHOSEN TO REPRESENT THE SOLUTION STRUCTURE.
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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