Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex


Tab-View Sample


T-Cell Epitope
Epitope  
   
Complex PDB ID 1KJ2
Accession Number 3DIEP0306
IEDB ID 34055
Epitope Sequence KVITFIDL
Starting Position1
Ending Position8
Epitope Type Linear Epitope

Assay Information  
Assay Antigen KVITFIDL GTP binding protein 1 Mus musculus"
PDB CategoryIMMUNE SYSTEM
Keyword T CELL RECEPTOR; CLASS I MHC; H-2KB; TCR-PMHC COMPLEX; ALLOGENEIC; 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 V module of the KB5-C20 TCR was produced in myeloma cells. There are two molecules in the crystallographic asymmetric unit. PDB chains for each complex are: Complex I MHC ?-chain: H; ?2-m chain: L; epitope chain: P; TCR ?-chain: A; TCR ?-chain: B. Complex II: MHC ?-chain: I; ?2-m chain: M; epitope chain: Q; TCR ?-chain: D; TCR ?-chain: E. The two complexes differ only by a 6 degrees rotation in the ?3/?2-m membrane-proximal domains.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.71
R-Value
0.219
Space Group
P 1 21 1
Unit Cell
Length(Å) Angle(°)
a = 89.2 α = 90
b = 77.92 β = 108.23
c = 132.96 γ = 90


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

Ligand non-polymer
 
Ligand NameN-ACETYL-D-GLUCOSAMINE
Chem Name NAG
Ligand NameALPHA-D-MANNOSE
Chem Name MAN
Ligand NameBETA-D-GALACTOSE
Chem Name GAL
Ligand NameO-SIALIC ACID
Chem Name SIA
Ligand NameN-ACETYL-D-GLUCOSAMINE
Chem Name NAG
Ligand NameALPHA-D-MANNOSE
Chem Name MAN
Ligand NameBETA-D-GALACTOSE
Chem Name GAL
Ligand NameO-SIALIC ACID
Chem Name SIA

Sequence


Protein Name
O-SIALIC ACID
Poly type
polypeptide(L)
Sequence status
Complete

Primary Sequence

Entity ID
1
Chain ID
H,I
Source Method
genetically manipulated
Molecule Name
Allogeneic H-2Kb MHC Class I Molecule
Fragment Name
Extracellular domains (alpha1, alpha2, alpha3)
Sequence Length
277

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

Entity ID
2
Chain ID
P
Source Method
Synthetic
Molecule Name
Naturally processed octapeptide PKB1
Sequence Length
8

K V I T F I D L
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)
Primary Sequence

Entity ID
3
Chain ID
L,M
Source Method
genetically manipulated
Molecule Name
Beta-2 microglobulin
Sequence Length
99

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

Entity ID
4
Chain ID
A,D
Source Method
genetically manipulated
Molecule Name
KB5-C20 T-Cell receptor alpha-chain
Fragment Name
Fv fragment , variable domain
Sequence Length
111

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

Entity ID
5
Chain ID
B,E
Source Method
genetically manipulated
Molecule Name
KB5-C20 T-Cell receptor beta-chain
Fragment Name
Fv fragment , variable domain
Sequence Length
117

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

X-RAY DIFFRACTION

Crystalization

pH
6.7
pH details
17-19% PEG 6000, 0.1M Mes, 0.1M NaCl, 0.1M MgAc, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
temparature
277
temparature Detail


Crystal Data
Unit Cell
Space group
P 1 21 1
Length
Angle
°
a  =
89.2
α  =
90
b  =
77.92
β  =
108.23
c  =
132.96
γ  =
90


Diffraction
Diffraction Detector
Diffraction radiation
Detector
IMAGE PLATE
Monochromator
Type
ESRF BEAMLINE BM30A
Diffraction Source
Detail
Source
SYNCHROTRON
Collection date
2/19/2000
Type
ESRF BEAMLINE BM30A


Refinement Data
Reflection Details
Structure Solution Method
MOLECULAR REPLACEMENT
Percent Possible(Observed)
Resolution(High)
2.71
R-Factor(Observed)
0.219
Cut-off Sigma(F)
0
R-Work
0.22
Number Reflections(Observed)
44772
R-Free
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
9919
Nucleic acid atom
0
Heterogen Atoms
134
Solvent Atoms
91
Total Atoms
10144


Software and Computing
Computing
Software
Data Reduction (intensity integration)
MOSFLM
model building
Data Reduction (data scaling)
CCP4 (SCALA)
refinement
CNS 0.9
Structure Solution
AMORE
Structure Refinement
CNS 0.9

GO functional annotation for 1kj2



Literature reference

Title
A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
The elongated complementary-determining region (CDR) 3beta found in the unliganded KB5-C20 TCR protrudes from the antigen binding site and prevents its docking onto the peptide/MHC (pMHC) surface according to a canonical diagonal orientation. We now present the crystal structure of a complex involving the KB5-C20 TCR and an octapeptide bound to the allogeneic H-2K(b) MHC class I molecule. This structure reveals how a tremendously large CDR3beta conformational change allows the KB5-C20 TCR to adapt to the rather constrained pMHC surface and achieve a diagonal docking mode. This extreme case of induced fit also shows that TCR plasticity is primarily restricted to CDR3 loops and does not propagate away from the antigen binding site.
PubMed ID
Search related article in PubMed
Keywords
T CELL RECEPTOR; CLASS I MHC; H-2KB; TCR-PMHC COMPLEX; ALLOGENEIC; IMMUNE SYSTEM




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


Ag-Ab Interaction of the1KJ2 between chain "P" and chain "A"



Jmol needs Java Runtime Environment to visualize the graphics. If you are not able to see the the graphics,
please update your Java Runtime Environment and refresh your browser.


Epitope found in chain   :P                                                                                           
Epitope Sequence:-KVITFIDL
Epitope Position found in PDB File   :   1-8  (Highlighted in white spacefill model)
K V I T F I D L

Download PDB File Download Ag-Ab Interaction PDB File
Upload a PDB file of your own:

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.
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.