1SJH Immune System date Mar 03, 2004
title Hla-Dr1 Complexed With A 13 Residue Hiv Capsid Peptide
authors Z.Zavala-Ruiz, I.Strug, B.D.Walker, P.J.Norris, L.J.Stern
compound source
Molecule: Hla Class II Histocompatibility Antigen, Dr Alpha Chain;
Chain: A
Fragment: Extracellular Domain Of Hla-Dra0101
Synonym: Mhc Class II Antigen Dra
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Dra
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: T7 Polymeraselac
Expression_system_plasmid: Plm1

Molecule: Hla Class II Histocompatibility Antigen, Drb1-1 Beta Chain;
Chain: B
Fragment: Extracellular Domain Of Hla-Drb0101
Synonym: Mhc Class I Antigen Drb11, Dr-1, Dr1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-Drb1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: T7 Polymeraselac
Expression_system_plasmid: Plm1

Molecule: Gag Polyprotein
Chain: C
Fragment: 13 Residue Peptide From Hiv-1 Gag Capsid Protein
Engineered: Yes

Synthetic: Yes
Other_details: Synthesized Peptide With Sequence From Human Immunodeficiency Virus Type 1 (Hiv-1) Gag Capsid Protein [166-178];

Molecule: Enterotoxin Type C-3
Chain: D
Fragment: Sec3 Variant 3b2
Synonym: Sec3
Engineered: Yes
Mutation: Yes

Organism_scientific: Staphylococcus Aureus
Organism_taxid: 1280
Gene: Entc3, Sav2009, Sa1817
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb2151
Expression_system_vector_type: Lac
symmetry Space Group: H 3
R_factor 0.220 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
172.464 172.464 121.461 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
related structures by homologous chain: 1I4Q, 1JWU, 1PYW, 1S9V
Gene
Ontology
ChainFunctionProcessComponent
A


B


D


Primary referenceA hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition., Zavala-Ruiz Z, Strug I, Walker BD, Norris PJ, Stern LJ, Proc Natl Acad Sci U S A 2004 Sep 7;101(36):13279-84. Epub 2004 Aug 26. PMID:15331779
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (1sjh.pdb1.gz) 318 Kb
  • CSU: Contacts of Structural Units for 1SJH
  • Likely Quarternary Molecular Structure file(s) for 1SJH
  • Structure Factors (521 Kb)
  • Retrieve 1SJH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SJH from S2C, [Save to disk]
  • Re-refined 1sjh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SJH 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 1SJH
  • 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 1SJH, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sjha2, region A:4-81 [Jmol] [rasmolscript] [script source]
        - Domain d1sjha1, region A:82-181 [Jmol] [rasmolscript] [script source]
        - Domain d1sjhb2, region B:1-92 [Jmol] [rasmolscript] [script source]
        - Domain d1sjhb1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1sjhd1, region D:1-121 [Jmol] [rasmolscript] [script source]
        - Domain d1sjhd2, region D:122-239 [Jmol] [rasmolscript] [script source]
  • Fold representative 1sjh 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: [1sjh] [1sjh_A] [1sjh_D] [1sjh_C] [1sjh_B]
  • SWISS-PROT database: [P04229] [P01903] [P0A0L5] [P12495]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [GAG_HV1Z2] by SWISSPFAM
  • Domains found in 1SJH: [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1SJH with the sequences similar proteins can be viewed for 1SJH's classification [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [GAG_HV1Z2] 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 [2B11_HUMAN] [DRA_HUMAN] [ENTC3_STAAU] [GAG_HV1Z2] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1SJH
  • Community annotation for 1SJH 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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