CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEPTOR; INFLUENZA HA ANTIGEN PEPTIDE; AND MHC CLASS II MOLECULE; HLA-DR1


Tab-View Sample


T-Cell Epitope
Epitope  
   
Complex PDB ID 1FYT
Accession Number 3DIEP0275
IEDB ID 48237
Epitope Sequence PKYVKQNTLKLAT
Starting Position306
Ending Position318
Epitope Type Linear Epitope

Assay Information  
Assay Antigen PKYVKQNTLKLAT Hemagglutinin precursor (322-334) Influenza A virus (A/Aichi/2/1968(H3N2))
PDB CategoryIMMUNE SYSTEM
Keyword protein-protein complex; immunoglobulin fold; IMMUNE SYSTEM
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain D
Antigen PDB ChainC
CommentsIn total; 7 of the 15 MHCII positions contacted to TCR in this complex are contacted in the D10/Tax/I-Ak complex [PDB: 1D9K]. The TCR-pMHC binding mode is close to that observed in the human B7 TCR/Tax/HLA-A2 complex [PDB: 1BD2].

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.6
R-Value
Space Group
C 1 2 1
Unit Cell
Length(Å) Angle(°)
a = 142.902 α = 90
b = 73.439 β = 108.23
c = 122.428 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION
Host OrganismDrosophila melanogaster
Host Taxonomic ID 7227

Ligand non-polymer
 
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
Source Method
genetically manipulated
Molecule Name
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
Fragment Name
EXTRACELLULAR DOMAIN
Sequence Length
181

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

Entity ID
2
Chain ID
B
Source Method
genetically manipulated
Molecule Name
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN
Fragment Name
EXTRACELLULAR DOMAIN
Sequence Length
192

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

Entity ID
3
Chain ID
C
Source Method
genetically manipulated
Molecule Name
HEMAGGLUTININ HA1 PEPTIDE CHAIN
Fragment Name
ANTIGEN PEPTIDE
Sequence Length
13

P K Y V K Q N T L K L A T
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)
Primary Sequence

Entity ID
4
Chain ID
D
Source Method
genetically manipulated
Molecule Name
T-CELL RECEPTOR ALPHA CHAIN
Fragment Name
EXTRACELLULAR DOMAIN
Sequence Length
212

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

Entity ID
5
Chain ID
E
Source Method
genetically manipulated
Molecule Name
T-CELL RECEPTOR BETA CHAIN
Fragment Name
EXTRACELLULAR DOMAIN
Sequence Length
245

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

X-RAY DIFFRACTION

Crystalization

pH
7
pH details
"11% PEG 8000, 1 M NaCl, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K"
temparature
18
temparature Detail


Crystal Data
Unit Cell
Space group
C 1 2 1
Length
Angle
°
a  =
142.902
α  =
90
b  =
73.439
β  =
108.23
c  =
122.428
γ  =
90


Diffraction
Diffraction Detector
Diffraction radiation
Detector
CCD
Monochromator
Type
APS BEAMLINE 14-BM-C
Diffraction Source
Detail
Source
SYNCHROTRON
Collection date
11/20/1999
Type
APS BEAMLINE 14-BM-C


Refinement Data
Reflection Details
Structure Solution Method
Percent Possible(Observed)
99.6
Resolution(High)
2.6
R-Factor(Observed)
Cut-off Sigma(F)
0
R-Work
0.221
Number Reflections(Observed)
37122
R-Free
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
6516
Nucleic acid atom
0
Heterogen Atoms
28
Solvent Atoms
100
Total Atoms
6644


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 1fyt

  Cellular component Chain(s)
  0016020  
  membrane
A, B 
  0019031  
  viral envelope
  0042613  
    MHC class II protein complex
A, B 
  Biological process Chain(s)
  0006955  
  immune response
A, B 
  0019882  
  antigen processing and presentation
A, B 
  0019064  
  viral envelope fusion with host membrane
  Biochemical function Chain(s)
  0046789  
  host cell surface receptor binding


Literature reference

Title
Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
An alphabeta T-cell receptor (alphabetaTCR)/hemagglutinin (HA) peptide/human leukocyte antigen (HLA)-DR1 complex was stabilized by flexibly linking the HA peptide with the human HA1.7 alphabetaTCR; to increase the local concentration of the interacting proteins once the peptide has been loaded onto the major histocompatibility complex (MHC) molecule. The structure of the complex; determined by X-ray crystallography; has a binding mode similar to that of the human B7 alphabetaTCR on a pMHCI molecule. Twelve of the 15 MHC residues contacted are at the same positions observed earlier in class I MHC/peptide/TCR complexes. One contact; to an MHC loop outside the peptide-binding site; is conserved and specific to pMHCII complexes. TCR gene usage in the response to HA/HLA-DR appears to conserve charged interactions between three lysines of the peptide and acidic residues on the TCR.
PubMed ID
Search related article in PubMed
Keywords
protein-protein complex; immunoglobulin fold; IMMUNE SYSTEM




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Ag-Ab Interaction of the1FYT between chain "C" and chain "D"



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Epitope found in chain   :C                                                                                           
Epitope Sequence:- PKYVKQNTLKLAT
Epitope Position found in PDB File   :   306-318  (Highlighted in white spacefill model)
P K Y V K Q N T L K L A T

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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.
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.