1RF3 Signaling Protein date Nov 07, 2003
title Structurally Distinct Recognition Motifs In Lymphotoxin-B Receptor And Cd40 For Traf-Mediated Signaling
authors C.Li, P.S.Norris, C.Z.Ni, M.L.Havert, E.M.Chiong, B.R.Tran, E.Cabezas, G.Cheng, J.C.Reed, A.C.Satterthwait, C.F.Ware, K.R.El
compound source
Molecule: Tnf Receptor Associated Factor 3
Chain: A
Fragment: Recognition Motif (Residues 377-568)
Synonym: Cd40 Receptor Associated Factor 1, Craf1, Cd40 Binding Protein, Cd40bp, Lmp1 Associated Protein, Lap1, Cap-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Traf3 Or Craf1 Or Cap1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 De3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21b

Molecule: 24-Residue Peptide From Lymphotoxin-B Receptor
Chain: B
Fragment: Recognition Motif (Residues 385-408)
Engineered: Yes

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized, The Sequence Of The Peptide Occurs Naturally In Humans (Homo Sapiens)
symmetry Space Group: P 3 2 1
R_factor 0.266 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.700 83.700 79.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.50 Å
Primary referenceStructurally distinct recognition motifs in lymphotoxin-beta receptor and CD40 for tumor necrosis factor receptor-associated factor (TRAF)-mediated signaling., Li C, Norris PS, Ni CZ, Havert ML, Chiong EM, Tran BR, Cabezas E, Reed JC, Satterthwait AC, Ware CF, Ely KR, J Biol Chem 2003 Dec 12;278(50):50523-9. Epub 2003 Sep 29. PMID:14517219
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (39 Kb) [Save to disk]
  • Biological Unit Coordinates (1rf3.pdb1.gz) 103 Kb
  • CSU: Contacts of Structural Units for 1RF3
  • Likely Quarternary Molecular Structure file(s) for 1RF3
  • Retrieve 1RF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RF3 from S2C, [Save to disk]
  • View 1RF3 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 1RF3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1RF3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rf3a2, region A:313-349 [Jmol] [rasmolscript] [script source]
        - Domain d1rf3a1, region A:350-504 [Jmol] [rasmolscript] [script source]
        - Domain d1rf3b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1e1rf3, region F:82-357 [Jmol] [rasmolscript] [script source]
  • Fold representative 1rf3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rf3] [1rf3_A] [1rf3_B]
  • SWISS-PROT database: [P36941] [Q13114]
  • Domain organization of [TNR3_HUMAN] [TRAF3_HUMAN] by SWISSPFAM
  • Domain found in 1RF3: [MATH ] by SMART
  • Other resources with information on 1RF3
  • Community annotation for 1RF3 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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