3M19 Immune System date Mar 04, 2010
title Crystal Structure Of Variable Lymphocyte Receptor Vlra.R5.1
authors L.Deng, C.A.Velikovsky, R.A.Mariuzza
compound source
Molecule: Variable Lymphocyte Receptor A Diversity Region
Chain: A, B
Fragment: Ectodomain
Engineered: Yes
 Organism_scientific: Petromyzon Marinus
Organism_common: Marine Lamprey
Organism_taxid: 7757
Gene: Vlra
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codonplus(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pt7-7
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.333 77.053 65.392 90.00 112.04 90.00
method X-Ray Diffractionresolution 1.70 Å
Primary referenceA structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey., Deng L, Velikovsky CA, Xu G, Iyer LM, Tasumi S, Kerzic MC, Flajnik MF, Aravind L, Pancer Z, Mariuzza RA, Proc Natl Acad Sci U S A. 2010 Jul 8. PMID:20616002
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3m19.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (3m19.pdb2.gz) 40 Kb
  • CSU: Contacts of Structural Units for 3M19
  • Structure Factors (439 Kb)
  • Retrieve 3M19 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M19 from S2C, [Save to disk]
  • Re-refined 3m19 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3M19 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 3M19
  • 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 3M19, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m19_B] [3m19] [3m19_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3M19: [LRRNT] [LRR_TYP ] by SMART
    • Other resources with information on 3M19
  • Community annotation for 3M19 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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