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- PDB-2kn1: Solution NMR Structure of BCMA -

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Basic information

Entry
Database: PDB / ID: 2kn1
TitleSolution NMR Structure of BCMA
ComponentsTumor necrosis factor receptor superfamily member 17
KeywordsSIGNALING PROTEIN / BCMA / BAFF / TNF Receptor / CRD / APRIL
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
Tumor necrosis factor receptor fold / Tumor necrosis factor receptor superfamily / BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPellegrini, M. / Willen, L. / Perroud, M. / Krushinskie, D. / Strauch, K. / Cuervo, H. / Sun, Y. / Day, E.S. / Schneider, P. / Zheng, T.S.
CitationJournal: Febs J. / Year: 2013
Title: Structure of the extracellular domains of human and Xenopus Fn14: implications in the evolution of TWEAK and Fn14 interactions.
Authors: Pellegrini, M. / Willen, L. / Perroud, M. / Krushinskie, D. / Strauch, K. / Cuervo, H. / Day, E.S. / Schneider, P. / Zheng, T.S.
History
DepositionAug 11, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3May 1, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 17


Theoretical massNumber of molelcules
Total (without water)5,6011
Polymers5,6011
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 / 10020 lowest energy structures
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 5601.405 Da / Num. of mol.: 1 / Fragment: residues 2-50 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q02223

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of the extracellular CRD domain of human BCMA (synthetic source)
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 900 uM BCMA, 10 mM sodium phosphate, 0.02 % sodium azide, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
900 uMBCMA-11
10 mMsodium phosphate-21
0.02 %sodium azide-31
Sample conditionsIonic strength: 10 / pH: 6.0 / Pressure: ambient / Temperature: 298-318 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.structure solution
SPARKY3.11Goddarddata analysis
CNS1.1Brunger A. T. et.al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 lowest energy structures / Conformers calculated total number: 100 / Conformers submitted total number: 20

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