1XU2 Cytokine, Hormone Growth Factor Receptor date Oct 25, 2004
title The Crystal Structure Of April Bound To Bcma
authors S.G.Hymowitz, D.R.Patel, H.J.A.Wallweber, S.Runyon, M.Yan, J.Yin, S.K.Shriver, N.C.Gordon, B.Pan, N.J.Skelton, R.F.Kelley, M.A.Sta
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, D
Fragment: Tnf Domain Of April
Synonym: A Proliferation-Inducing Ligand, April, Tnfsf13b O
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Tnfsf13, April
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a (Modified)

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: R, S, T
Fragment: Bcma Ecd
Synonym: B-Cell Maturation Protein, Tnffsf17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf17, Bcm, Bcma
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pzct
symmetry Space Group: P 61
R_factor 0.178 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
114.294 114.294 91.180 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.35 Å
ligand NI enzyme
related structures by homologous chain: 1OQD, 1U5Y, 1U5Z
Gene
Ontology
ChainFunctionProcessComponent
A, D, B


S, T, R


Primary referenceStructures of APRIL-receptor complexes: Like BCMA, TACI employs only a single cysteine-rich domain for high-affinity ligand binding., Hymowitz SG, Patel DR, Wallweber HJ, Runyon S, Yan M, Yin J, Shriver SK, Gordon NC, Pan B, Skelton NJ, Kelley RF, Starovasnik MA, J Biol Chem 2004 Nov 12;. PMID:15542592
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (89 Kb) [Save to disk]
  • Biological Unit Coordinates (1xu2.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 1XU2
  • CSU: Contacts of Structural Units for 1XU2
  • Likely Quarternary Molecular Structure file(s) for 1XU2
  • Structure Factors (207 Kb)
  • Retrieve 1XU2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XU2 from S2C, [Save to disk]
  • Re-refined 1xu2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1XU2 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1XU2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1XU2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1xu2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1xu2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1xu2d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1xu2r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1xu2s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1xu2t_, region T [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xu2_S] [1xu2_D] [1xu2_A] [1xu2_T] [1xu2] [1xu2_B] [1xu2_R]
  • SWISS-PROT database: [Q9D777] [Q02223]
  • Domain organization of [TNF13_MOUSE] [TNR17_HUMAN] by SWISSPFAM
  • Domain found in 1XU2: [TNF ] by SMART
    • Other resources with information on 1XU2
  • Community annotation for 1XU2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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