CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA


Tab-View Sample


T-Cell Epitope
Epitope  
   
Complex PDB ID 1D9K
Accession Number 3DIEP0291
IEDB ID 83218
Epitope Sequence HRGAIEWEGIESG
Starting Position134
Ending Position146
Epitope Type Linear Epitope

Assay Information  
Assay Antigen HRGAIEWEGIESG Ovotransferrin precursor (Conalbumin) (Serum transferrin) (Allergen Gal d 3) (Allergen Gal d III) Gallus gallus
PDB CategoryIMMUNE SYSTEM
Keyword T-CELL RECEPTOR; MHC CLASS II; D10; I-AK; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain A
Antigen PDB ChainP
CommentsThe crystal structure contains the MHC/epitope complex bound to V module of TCR D10; derived from AKR/J (H-2k) mouse T cell clone D10.G4. There are two complexes in the crystallographic asymmetric unit; related to each other by a 115 degree rotation. PDB chains for each complex are: Complex I: MHC ?-chain: C; MHC ?-chain: D; epitope chain: P; TCR ?-chain: A; TCR ?-chain: B; Complex II: MHC ?-chain: G; MHC ?-chain: H; epitope chain: Q; TCR ?-chain: E; TCR ?-chain: F. The two complexes are very similar and only complex I is discussed in the analysis. The final model includes residues 1-182 and 2-190 of MHC ? and ? chains; respectively; all 16 epitope residues and residues 2-117; 3-116 of TCR V? and V? domains; respectively.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
3.2
R-Value
0.07
Space Group
P 21 21 2
Unit Cell
Length(Å) Angle(°)
a = 97.6 α = 90
b = 345.3 β = 90
c = 97.7 γ = 90



Source Information  
Structure Determination Method X-RAY DIFFRACTION
Host OrganismEscherichia coli
Host Taxonomic ID 562
PlasmidPET-11A
  

Ligand D-saccharide
 
Ligand Name2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Chem Name NDG
Ligand NameN-ACETYL-D-GLUCOSAMINE
Chem Name NAG
Ligand Name2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Chem Name NDG
Ligand NameN-ACETYL-D-GLUCOSAMINE
Chem Name NAG

Sequence


Protein Name
N-ACETYL-D-GLUCOSAMINE
Poly type
polypeptide(L)
Sequence status
Complete

Primary Sequence

Entity ID
1
Chain ID
A,E
Source Method
genetically manipulated
Molecule Name
T-CELL RECEPTOR D10 (ALPHA CHAIN)
Sequence Length
110

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

Entity ID
2
Chain ID
B,F
Source Method
genetically manipulated
Molecule Name
T-CELL RECEPTOR D10 (BETA CHAIN)
Sequence Length
112

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

Entity ID
3
Chain ID
C,G
Source Method
genetically manipulated
Molecule Name
MHC I-AK A CHAIN (ALPHA CHAIN)
Sequence Length
183

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

Entity ID
4
Chain ID
D,H
Source Method
genetically manipulated
Molecule Name
MHC I-AK B CHAIN (BETA CHAIN)
Sequence Length
188

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

Entity ID
5
Chain ID
P,Q
Source Method
genetically manipulated
Molecule Name
CONALBUMIN PEPTIDE
Sequence Length
16

G N S H R G A I E W E G I E S G
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)

X-RAY DIFFRACTION

Crystalization

pH
8.5
pH details
PEG 8000, sodium chloride, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
temparature
298
temparature Detail


Crystal Data
Unit Cell
Space group
P 21 21 2
Length
Angle
°
a  =
97.6
α  =
90
b  =
345.3
β  =
90
c  =
97.7
γ  =
90


Diffraction
Diffraction Detector
Diffraction radiation
Detector
CCD
Monochromator
Type
APS BEAMLINE 19-ID
Diffraction Source
Detail
Source
SYNCHROTRON
Collection date
4/12/1999
Type
APS BEAMLINE 19-ID


Refinement Data
Reflection Details
Structure Solution Method
molecular replacement
Percent Possible(Observed)
95.2
Resolution(High)
3.2
R-Factor(Observed)
0.07
Cut-off Sigma(F)
0
R-Work
0.247
Number Reflections(Observed)
46332
R-Free
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
9822
Nucleic acid atom
0
Heterogen Atoms
140
Solvent Atoms
0
Total Atoms
9962


Software and Computing
Computing
Software
Data Reduction (intensity integration)
DENZO
model building
Data Reduction (data scaling)
SCALEPACK
refinement
X-PLOR 3.1
Structure Solution
AMORE
Structure Refinement
X-PLOR 3.1

GO functional annotation for 1d9k

  Cellular component Chain(s)
  0016020  
  membrane
C, D, G, H 
  0042613  
    MHC class II protein complex
C, D, G, H 
  Biological process Chain(s)
  0006955  
  immune response
C, D, G, H 
  0019882  
  antigen processing and presentation
C, D, G, H 


Literature reference

Title
The crystal structure of a T cell receptor in complex with peptide and MHC class II.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
The crystal structure of a complex involving the D10 T cell receptor (TCR); 16-residue foreign peptide antigen; and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand; necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently; the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation; although with substantial variability. Peptide recognition; which involves P-1 to P8 residues; is dominated by the Valpha domain; which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects; suggests a structural basis for alloreactivity; and illustrates how bacterial superantigens can span the TCR-pMHCII surface.
PubMed ID
Search related article in PubMed
Keywords
T-CELL RECEPTOR; MHC CLASS II; D10; I-AK; IMMUNE SYSTEM




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Ag-Ab Interaction of the1D9K between chain "P" and chain "A"



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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.
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.