2JY8 Protein Binding date Dec 07, 2007
title Nmr Structure Of The Ubiquitin Associated (Uba) Domain Of P62 (Sqstm1) In Complex With Ubiquitin. Rdc Refined
authors J.E.Long, R.Layfield, M.S.Searle
compound source
Molecule: Ubiquitin-Binding Protein P62
Chain: A
Fragment: Uba Domain
Synonym: Sequestosome-1, Phosphotyrosine-Independent Ligand For The Lck Sh2 Domain Of 62 Kda, Ebi3-Associated Protein Of 60 Kda, P60, Ebiap;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sqstm1, Orca, Osil
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21
Expression_system_variant: (De3)
Expression_system_vector_type: Vector
Expression_system_vector: Pgex-4t-1
methodSolution NMR
Primary referenceUbiquitin Recognition by the Ubiquitin-associated Domain of p62 Involves a Novel Conformational Switch., Long J, Gallagher TR, Cavey JR, Sheppard PW, Ralston SH, Layfield R, Searle MS, J Biol Chem. 2008 Feb 29;283(9):5427-5440. Epub 2007 Dec 14. PMID:18083707
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 2JY8
  • Original NMR restraints for 2JY8 from PDB
  • Retrieve 2JY8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JY8 from S2C, [Save to disk]
  • View 2JY8 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 2JY8
  • 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 2JY8, from MSDmotif at EBI
  • Fold representative 2jy8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jy8] [2jy8_A]
  • SWISS-PROT database: [Q13501]
  • Domain organization of [SQSTM_HUMAN] by SWISSPFAM
  • Domain found in 2JY8: [UBA ] by SMART
  • Alignments of the sequence of 2JY8 with the sequences similar proteins can be viewed for 2JY8's classification [SQSTM_HUMAN] 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 [SQSTM_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2JY8
  • Community annotation for 2JY8 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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