CRYSTAL STRUCTURE OF THE HUMAN CLASS II MHC PROTEIN HLA-DR1 COMPLEXED WITH AN INFLUENZA VIRUS PEPTIDE


Tab-View Sample


MHC-Binding
Epitope  
   
Complex PDB ID 1DLH
Accession Number 3DIEP0345
IEDB ID 30016
Epitope Sequence PKYVKQNTLKLAT
Starting Position306
Ending Position318
Epitope Type Linear Epitope

Assay Information  
Assay Antigen "Purified MHC - X-ray crystallography Structure (crystal; NMR; etc.)"
PDB CategoryHISTOCOMPATIBILITY ANTIGEN
Keyword HISTOCOMPATIBILITY ANTIGEN
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain A
Antigen PDB ChainC
CommentsAmongst MHC residues interacting with peptide; the residues that do not directly contact the peptide but are inaccessible to solvent are listed as well (residues of the chain A: I7; A61; and chain B: L26; C30; V38; K65; T77). Hydrogen bonds between MHC and only the peptide main chain are provided in the paper.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
R-Value
0.205
R-Free
0.304
Space Group
P 43 21 2
Unit Cell
Length(Å) Angle(°)
a = 94.6 α = 90
b = 94.6 β = 90
c = 247.5 γ = 90


Source Information  
Structure Determination Method X-RAY DIFFRACTION
Host OrganismSpodoptera
Host Taxonomic ID 7106

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

Sequence


Protein Name
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Poly type
polypeptide(L)
Sequence status
Complete

Primary Sequence

Entity ID
1
Chain ID
A,D
Source Method
genetically manipulated
Molecule Name
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (ALPHA CHAIN)
Sequence Length
180

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 A
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
CLASS II HISTOCOMPATIBILITY ANTIGEN (HLA-DR1) (BETA CHAIN)
Sequence Length
188

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
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
genetically manipulated
Molecule Name
ENTEROTOXIN TYPE B PRECURSOR
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)

X-RAY DIFFRACTION

Crystalization

pH details


Crystal Data
Unit Cell
Space group
P 43 21 2
Length
Angle
°
a  =
94.6
α  =
90
b  =
94.6
β  =
90
c  =
247.5
γ  =
90


Diffraction
Diffraction Detector
Diffraction radiation
Detector
Monochromator
Type
Diffraction Source
Detail
Source
Collection date
Type


Refinement Data
Reflection Details
Structure Solution Method
Percent Possible(Observed)
Resolution(High)
R-Factor(Observed)
0.205
Cut-off Sigma(F)
R-Work
0.205
Number Reflections(Observed)
R-Free
0.304
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
6255
Nucleic acid atom
0
Heterogen Atoms
112
Solvent Atoms
153
Total Atoms


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

GO functional annotation for 1dlh



Literature reference

Title
Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
LCMV infection of H-2(b) mice generates a CD8(+) CTL response mainly directed toward three immunodominant epitopes. One of these; gp33; is presented by both H-2D(b) and H-2K(b) MHC class I molecules. The virus can escape immune recognition in the context of both these MHC class I molecules through single mutations of the peptide. In order to understand the underlying structural mechanism; we determined the crystal structures of both complexes. The structures reveal that the peptide is presented in two diametrically opposed manners by H-2D(b) and H-2K(b); with residues used as anchor positions in one MHC class I molecule interacting with the TCR in the other. Importantly; the peptide's N-terminal residue p1K protrudes from the binding cleft in H-2K(b). We present structural evidence that explains the functional consequences of single mutations found in escape variants.
PubMed ID
Search related article in PubMed
Keywords
HISTOCOMPATIBILITY ANTIGEN




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Ag-Ab Interaction of the1DLH between chain "C" and chain "A"



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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.