3MOP Signaling Protein, Immune System date Apr 23, 2010
title The Ternary Death Domain Complex Of Myd88, Irak4, And Irak2
authors S.C.Lin, Y.C.Lo, H.Wu
compound source
Molecule: Myeloid Differentiation Primary Response Protein
Chain: A, B, C, D, E, F
Fragment: Death Domain Residues 20-117
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Myd88
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Interleukin-1 Receptor-Associated Kinase 4
Chain: G, H, I, J
Fragment: Death Domain Residues 4-106
Synonym: Irak-4, Renal Carcinoma Antigen Ny-Ren-64
Ec: 2.7.11.1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Irak4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a

Molecule: Interleukin-1 Receptor-Associated Kinase-Like 2
Chain: K, L, M, N
Fragment: Death Domain Residues 2-112
Synonym: Irak-2
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Irak2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a
symmetry Space Group: C 2 2 21
R_factor 0.216 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
101.709 307.116 187.619 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand
enzyme Transferase E.C.2.7.11.1 BRENDA
note 3MOP is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
F, A, N, K, E, B, M, C, D, L


Primary referenceHelical assembly in the MyD88-IRAK4-IRAK2 complex in TLR/IL-1R signalling., Lin SC, Lo YC, Wu H, Nature. 2010 May 19. PMID:20485341
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (514 Kb) [Save to disk]
  • Biological Unit Coordinates (3mop.pdb1.gz) 505 Kb
  • CSU: Contacts of Structural Units for 3MOP
  • Structure Factors (527 Kb)
  • Retrieve 3MOP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MOP from S2C, [Save to disk]
  • Re-refined 3mop structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MOP 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 3MOP
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3MOP, from MSDmotif at EBI
  • Fold representative 3mop from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mop_F] [3mop_M] [3mop_I] [3mop_C] [3mop] [3mop_K] [3mop_L] [3mop_B] [3mop_H] [3mop_E] [3mop_A] [3mop_J] [3mop_D] [3mop_G] [3mop_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3MOP: [DEATH ] by SMART
  • Alignments of the sequence of 3MOP with the sequences similar proteins can be viewed for 3MOP's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3MOP
  • Community annotation for 3MOP 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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