1J5N Dna Binding Protein Dna date May 15, 2002
title Solution Structure Of The Non-Sequence-Specific Hmgb Protein Nhp6a In Complex With Sry Dna
authors J.E.Masse, B.Wong, Y.M.Yen, F.H.T.Allain, R.C.Johnson, J.Feigon
compound source
Molecule: Nonhistone Chromosomal Protein 6a
Chain: A
Synonym: Nhp6a
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'- D(Gpgpgpgptpgpaptptpgptptpcpapg)-3';
Chain: B
Engineered: Yes
Other_details: Sry_dna G-Rich Strand

Synthetic: Yes
Other_details: Unlabeled Dna Made On A Commercial Synthesizer, 15n,13c-Labeled Dna Made Enzymatically In Vitro With Taq Polymerase;

Molecule: 5'- D(Cptpgpapapcpapaptpcpapcpcpcpc)-3';
Chain: C
Engineered: Yes
Other_details: Sry_dna C-Rich Strand

Synthetic: Yes
Other_details: Unlabeled Dna Made On A Commercial Synthesizer, 15n,13c-Labeled Dna Made Enzymatically In Vitro With Taq Polymerase
methodSolution NMR
related structures by homologous chain: 1CG7
  • MutSalpha complex binding

  • Primary referenceThe S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding., Masse JE, Wong B, Yen YM, Allain FH, Johnson RC, Feigon J, J Mol Biol 2002 Oct 18;323(2):263-84. PMID:12381320
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (835 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1J5N
  • Original NMR restraints for 1J5N from PDB
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1J5N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1J5N from S2C, [Save to disk]
  • View 1J5N 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 1J5N
  • 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 1J5N, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1j5na_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1j5n 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: [1j5n_A] [1j5n_C] [1j5n_B] [1j5n]
  • SWISS-PROT database: [P11632]
  • Domain organization of [NHP6A_YEAST] by SWISSPFAM
  • Domain found in 1J5N: [HMG ] by SMART
  • Other resources with information on 1J5N
  • Community annotation for 1J5N at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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