CRYSTAL STRUCTURE OF HLA-A*0201/OCTAMERIC TAX PEPTIDE COMPLEX


Tab-View Sample


MHC-Binding
Epitope  
   
Complex PDB ID 1DUY
Accession Number 3DIEP0482
IEDB ID 35844
Epitope Sequence LFGYPVYV
Starting Position2
Ending Position9
Epitope Type Linear Epitope

Assay Information  
Assay Antigen Purified MHC - X-ray crystallography Structure (crystal; NMR; etc.)
PDB CategoryIMMUNE SYSTEM
Keyword Immunoglobulin fold; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain A
Antigen PDB ChainC
CommentsThere are two molecules in the crystallographic asymmetric unit. PDB chains for each complex are: Complex I : MHC ?-chain: A; ?2-m chain: B; epitope chain: C. Complex II : MHC ?-chain: D; ?2-m chain: E; epitope chain: F.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.15
R-Value
0.198
Space Group
P 1
Unit Cell
Length(Å) Angle(°)
a = 50.34 α = 82.01
b = 62.86 β = 76.1
c = 74.84 γ = 77.96


Source Information  
Structure Determination Method X-RAY DIFFRACTION
Host OrganismEscherichia coli
Host Taxonomic ID 562

Ligand non-polymer
 

Sequence


Protein Name
CRYSTAL STRUCTURE OF HLA-A*0201/OCTAMERIC TAX PEPTIDE COMPLEX
Poly type
polypeptide(L)
Sequence status
Complete

Primary Sequence

Entity ID
1
Chain ID
A,D
Source Method
genetically manipulated
Molecule Name
HLA-A2*0201
Fragment Name
HEAVY CHAIN
Sequence Length
275

G S H S M R Y F F T S V S R P G R G E P R F I A V G Y V D D T Q F V R F D S D A A S Q R M E P R A P W I E Q E G P E Y W D G E T R K V K A H S Q T H R V D L G T L R G Y Y N Q S E A G S H T V Q R M Y G C D V G S D W R F L R G Y H Q Y A Y D G K D Y I A L K E D L R S W T A A D M A A Q T T K H K W E A A H V A E Q L R A Y L E G T C V E W L R R Y L E N G K E T L Q R T D A P K T H M T H H A V S D H E A T L R C W A L S F Y P A E I T L T W Q R D G E D Q T Q D T E L V E T R P A G D G T F Q K W A A V V V P S G Q E Q R Y T C H V Q H E G L P K P L T L R W E
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)
Primary Sequence

Entity ID
2
Chain ID
B,E
Source Method
genetically manipulated
Molecule Name
BETA-2 MICROGLOBULIN
Sequence Length
100

M I Q R T P K I Q V Y S R H P A E N G K S N F L N C Y V S G F H P S D I E V D L L K N G E R I E K V E H S D L S F S K D W S F Y L L Y Y T E F T P T E K D E Y A C R V N H V T L S Q P K I V K W D R D M
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)
Primary Sequence

Entity ID
3
Chain ID
C,F
Source Method
Synthetic
Molecule Name
HTLV-1 OCTAMERIC TAX PEPTIDE
Sequence Length
8

L F G Y P V Y V
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)

X-RAY DIFFRACTION

Crystalization

pH
6.5
pH details
13-20% polyethylene glycol 6000, 25 mM MES buffer, pH 6.5, VAPOR DIFFUSION, temperature 298K
temparature
298
temparature Detail


Crystal Data
Unit Cell
Space group
P 1
Length
Angle
°
a  =
50.34
α  =
82.01
b  =
62.86
β  =
76.1
c  =
74.84
γ  =
77.96


Diffraction
Diffraction Detector
Diffraction radiation
Detector
IMAGE PLATE
Monochromator
Type
ELLIOTT GX-13
Diffraction Source
Detail
Source
ROTATING ANODE
Collection date
11/27/1997
Type
ELLIOTT GX-13


Refinement Data
Reflection Details
Structure Solution Method
Percent Possible(Observed)
78
Resolution(High)
2.15
R-Factor(Observed)
0.198
Cut-off Sigma(F)
0
R-Work
0.192
Number Reflections(Observed)
38048
R-Free
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
6306
Nucleic acid atom
0
Heterogen Atoms
0
Solvent Atoms
495
Total Atoms
6801


Software and Computing
Computing
Software
Data Reduction (intensity integration)
DENZO
model building
Data Reduction (data scaling)
SCALEPACK
refinement
CNS 0.9
Structure Solution
AMORE
Structure Refinement
CNS 0.9

GO functional annotation for 1duy



Literature reference

Title
The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
The crystal structure of the human class I MHC molecule HLA-A2 complexed with of an octameric peptide; Tax8 (LFGYPVYV); from human T cell lymphotrophic virus-1 (HTLV-1) has been determined. This structure is compared with a newly refined; higher resolutio
PubMed ID
Search related article in PubMed
Keywords
Immunoglobulin fold; IMMUNE SYSTEM




If you are not able to view this pdf please update your Acrobat reader- click here


Ag-Ab Interaction of the1DUY between chain "C" and chain "A"



Download PDB File Download Ag-Ab Interaction PDB File

Aceess tip: Right-mouse click on Jmol to get access to additional Jmol functionality.

For more information or jmol tutorial please click here

Reference :
Herraez, Angel (2006), "Biomolecules in the Computer: Jmol to the Rescue", Biochemistry and Molecular Biology Education 34 (4): 255-261.



Links to external databases and resources



The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. Curation of peptidic epitope data relating to all infectious diseases.
Bcipep is collection of the peptides having the role in Humoral immunity. The peptides in the database has varying measure of immunogenicity.This database can assist in the development of method for predicting B cell epitopes, desigining synthetic vaccines and in disease diagnosis.
A DATABASE OF MHC LIGANDS AND PEPTIDE MOTIFS (Ver. 1.0) SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only.
The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. The website also gives access to a large number of tools that can be used to analyze these data. This project is funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID), a part of the National Institutes of Health (NIH). Click on any of the links below to access a database.
The aim of ABCpred server is to predict B cell epitope(s) in an antigen sequence, using artificial neural network. This is the first server developed based on recurrent neural network (machine based technique) using fixed length patterns.
EPIPREDICT is a new and reliable software to predict HLA-class II restricted T cell epitopes and ligands.
Expasy ProtScale ProtScale [Reference / Documentation] allows you to compute and represent the profile produced by any amino acid scale on a selected protein.
MHCBN is a curated database consisting of detailed information about major histocompatibility complex (MHC) binding, non-binding peptides, and T-cell epitopes. Version 4.0 provides information about peptides interacting with TAP and MHC-linked autoimmune diseases.
AntiJen v2.0 is a database containing quantitative binding data for peptides binding to MHC ligands, TCR-MHC complexes, T cell epitopes, TAP, B cell epitope molecules, and immunological protein-protein interactions. AntiJen includes a peptide library, copy numbers, and diffusion coefficient data. All entries are from published experimentally determined data. The database currently holds over 24,000 entries. No data in AntiJen is from prediction experiments.
HLA Peptide Binding Predictions Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature by Dr. Kenneth Parker, Children's Hospital Boston (email: kenneth.parker@childrens.harvard.edu ). Another web site for predicting which peptides bind to MHC molecules is SYFPEITHI, developed by Hans-Georg Rammensee's lab.
AllergenOnline provides access to a peer reviewed allergen list and sequence searchable database intended for identifying proteins that may present a potential risk of allergenic cross-reactivity. This website was designed to help in assessing the safety of proteins that may be introduced into foods through genetic engineering or food processing methods.
The I.U.I.S. Allergen Nomenclature Sub-committee operates under the auspices of the International Union of Immunological Societies (I.U.I.S.) and the World Health Organisation (W.H.O.). The objectives of the I.U.I.S. Allergen Nomenclature Sub-committee are to Maintain a unique and unambiguous nomenclature for allergen molecules and Maintain the ‘official list of allergens’.
Superficial is tool for the identification of potential epitopes or binding sites.
UMAS is a server which provides mirrors of a list of various epitope prediction tools and databases.
MAPPP will predict possible antigenic peptides to be processed and finally presented on cell surfaces. This database aides in the prediction of immunodominant T-cell epitopes and is able to predict the proteasomal cleavage of proteins into smaller fragments, and the binding of peptide sequences to MHC class I molecules.
JenPepM is a database of quantitative binding data for immunological protein-peptide interactions, which allows speedy access to binding data through simple on-line interfaces and effective search mechanisms.
Protall database contains biochemical and clinical information about plant food allergens involved in classical IgE-induced hypersensitivity reactions about 77 allergens from 48 plant species. There are many foods for which a case history of an allergic reaction has been reported for which the allergens responsible have not been described. These are not included in the database.
IMGT®, the international ImMunoGeneTics information system is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species.