2YHF Immune System date Apr 30, 2011
title 1.9 Angstrom Crystal Structure Of Clec5a
authors A.A.Watson, A.A.Lebedev, G.M.Murshudov, A.A.Vagin, B.A.Hall, C.A.O'Callaghan
compound source
Molecule: C-Type Lectin Domain Family 5 Member A
Chain: A, B, C, D, E, F, G, H, I
Fragment: Residues 70-187
Synonym: C-Type Lectin Superfamily Member 5, Myeloid Dap12- Associating Lectin 1, Mdl-1, Cl3;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: Peripheral Blood Mononuclear Cells
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pgmt7
symmetry Space Group: P 31
R_factor 0.216 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.109 109.109 84.879 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
Primary referenceStructural flexibility of the macrophage dengue virus receptor CLEC5A: Implications for ligand binding and signaling., Watson AA, Lebedev AA, Hall BA, Fenton-May AE, Vagin AA, Dejnirattisai W, Felce J, Mongkolsapaya J, Palma AS, Liu Y, Feizi T, Screaton GR, Murshudov GN, O'Callaghan CA, J Biol Chem. 2011 May 12. PMID:21566123
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (195 Kb) [Save to disk]
  • Biological Unit Coordinates (2yhf.pdb1.gz) 25 Kb
  • Biological Unit Coordinates (2yhf.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (2yhf.pdb3.gz) 24 Kb
  • Biological Unit Coordinates (2yhf.pdb4.gz) 24 Kb
  • Biological Unit Coordinates (2yhf.pdb5.gz) 25 Kb
  • Biological Unit Coordinates (2yhf.pdb6.gz) 25 Kb
  • Biological Unit Coordinates (2yhf.pdb7.gz) 24 Kb
  • Biological Unit Coordinates (2yhf.pdb8.gz) 25 Kb
  • Biological Unit Coordinates (2yhf.pdb9.gz) 23 Kb
  • CSU: Contacts of Structural Units for 2YHF
  • Structure Factors (609 Kb)
  • Retrieve 2YHF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YHF from S2C, [Save to disk]
  • Re-refined 2yhf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YHF 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 2YHF
  • 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 2YHF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yhf_G] [2yhf_D] [2yhf_B] [2yhf_I] [2yhf_E] [2yhf_A] [2yhf_C] [2yhf_F] [2yhf_H] [2yhf]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YHF: [CLECT ] by SMART
  • Other resources with information on 2YHF
  • Community annotation for 2YHF 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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