1KG0 Viral Protein Immune System date Nov 25, 2001
title Structure Of The Epstein-Barr Virus Gp42 Protein Bound To The Mhc Class II Receptor Hla-Dr1
authors M.M.Mullen, K.M.Haan, R.Longnecker, T.S.Jardetzky
compound source
Molecule: Mhc Class II Receptor Hla-Dr1
Chain: A
Fragment: Alpha Chain, Extracellular Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Mhc Class II Receptor Hla-Dr1
Chain: B
Fragment: Beta Chain, Extracellular Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Hemagglutinin Ha Peptide
Chain: D
Fragment: Antigenic Peptide
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Derived From Influenza Hemagglutinin Sequence;

Molecule: Gp42 Protein
Chain: C
Fragment: Extracellular Domain
Engineered: Yes

Organism_scientific: Human Herpesvirus 4
Organism_common: Epstein-Barr Virus
Organism_taxid: 10376
Strain: Gd1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pbac-Gus3
symmetry Space Group: P 63 2 2
R_factor 0.221 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
170.400 170.400 101.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.65 Å
related structures by homologous chain: 1IAO, 1JWM, 1R5I
Primary referenceStructure of the Epstein-Barr virus gp42 protein bound to the MHC class II receptor HLA-DR1., Mullen MM, Haan KM, Longnecker R, Jardetzky TS, Mol Cell 2002 Feb;9(2):375-85. PMID:11864610
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (1kg0.pdb1.gz) 100 Kb
  • CSU: Contacts of Structural Units for 1KG0
  • Likely Quarternary Molecular Structure file(s) for 1KG0
  • Retrieve 1KG0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KG0 from S2C, [Save to disk]
  • View 1KG0 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 1KG0
  • 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 1KG0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kg0a2, region A:3-81 [Jmol] [rasmolscript] [script source]
        - Domain d1kg0a1, region A:82-182 [Jmol] [rasmolscript] [script source]
        - Domain d1kg0b2, region B:3-92 [Jmol] [rasmolscript] [script source]
        - Domain d1kg0b1, region B:93-190 [Jmol] [rasmolscript] [script source]
        - Domain d1kg0c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1kg0 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: [1kg0_D] [1kg0_A] [1kg0_C] [1kg0] [1kg0_B]
  • SWISS-PROT database: [P04229] [P01903] [P03205]
  • Domain organization of [2B11_HUMAN] [DRA_HUMAN] [GP42_EBVB9] by SWISSPFAM
  • Domains found in 1KG0: [CLECT] [IGc1] [MHC_II_alpha] [MHC_II_beta ] by SMART
  • Alignments of the sequence of 1KG0 with the sequences similar proteins can be viewed for 1KG0's classification [2B11_HUMAN] [DRA_HUMAN] [GP42_EBVB9] 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] [GP42_EBVB9] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1KG0
  • Community annotation for 1KG0 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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