THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3


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MHC-Binding
Epitope  
   
Complex PDB ID 1A6A
Accession Number 3DIEP0395
IEDB ID 38564
Epitope Sequence PVSKMRMATPLLMQA
Starting Position87
Ending Position101
Epitope Type Linear Epitope

Assay Information  
Assay Antigen Purified MHC - X-ray crystallography Structure (crystal; NMR; etc.)
PDB CategoryCOMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)
Keyword MHC GLYCOPROTEIN; COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)
Antibody Residues Interacting with Antigen Open in new window      Download dimplot pdb file
Antibody Chain 1 PDB Chain A
Antigen PDB ChainC
CommentsResidues PVSKMRMATPLLMQA are the region observed in the crystal structure. N- and C-terminal residues in the peptide are disordered and not observable in the crystal structure.

Experimental Details
Method
X-RAY DIFFRACTION
Resolution
2.75
R-Value
0.246
Space Group
P 32 1 2
Unit Cell
Length(Å) Angle(°)
a = 78.45 α = 90
b = 78.45 β = 90
c = 159.1 γ = 120


Source Information  
Structure Determination Method X-RAY DIFFRACTION
Source Organism Homo sapiens
Common Namehuman
Taxonomic ID9606
Source Organism Homo sapiens
Common Namehuman
Taxonomic ID9606
Source Organism Homo sapiens
Common Namehuman
Taxonomic ID9606
Entity ID3

Sequence


Protein Name
THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
Poly type
polypeptide(L)
Sequence status
Complete

Primary Sequence

Entity ID
1
Chain ID
A
Source Method
Natural
Molecule Name
HLA class II histocompatibility antigen, DR alpha chain
Sequence Length
176

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
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)
Primary Sequence

Entity ID
2
Chain ID
B
Source Method
Natural
Molecule Name
HLA class II histocompatibility antigen, DR-1 beta chain
Sequence Length
187

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

Entity ID
3
Chain ID
C
Source Method
Natural
Molecule Name
HLA class II histocompatibility antigen, gamma chain
Fragment Name
CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN
Sequence Length
15

P V S K M R M A T P L L M Q A
The amino acid color is based upon Bob Fletterick's 'Shapely Models'.(Ref. & Table)

X-RAY DIFFRACTION

Crystalization

pH
4.5
pH details
12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5


Crystal Data
Unit Cell
Space group
P 32 1 2
Length
Angle
°
a  =
78.45
α  =
90
b  =
78.45
β  =
90
c  =
159.1
γ  =
120


Diffraction
Diffraction Detector
Diffraction radiation
Detector
IMAGE PLATE
Monochromator
SI(111)
Type
CHESS BEAMLINE F1
Diffraction Source
Detail
MIRRORS
Source
SYNCHROTRON
Collection date
1994-07
Type
CHESS BEAMLINE F1


Refinement Data
Reflection Details
Structure Solution Method
MOLECULAR REPLACEMENT
Percent Possible(Observed)
97.9
Resolution(High)
2.75
R-Factor(Observed)
0.246
Cut-off Sigma(F)
0
R-Work
0.246
Number Reflections(Observed)
13095
R-Free
No. of Non-Hydrogen atoms
Used in Refinement
Protein atom
3111
Nucleic acid atom
0
Heterogen Atoms
28
Solvent Atoms
22
Total Atoms
3161


Software and Computing
Computing
Software
Data Reduction (intensity integration)
DENZO
model building
SI(111)
Data Reduction (data scaling)
CCP4 (AGROVATA, ROTAVATA)
refinement
X-PLOR 3.1
Structure Solution
AMORE
Structure Refinement
X-PLOR 3.1

GO functional annotation for 1a6a

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


Literature reference

Title
The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.
Authors
Journal
Year
Journal Volume
First Page
Last Page
PubMed Abstract
A complex between HLA-DR3 and a fragment of invariant chain called CLIP was isolated from a human cell line defective in antigen presentation and its X-ray crystal structure determined. Previous data indicate that this complex is an intermediate in class II histocompatibility maturation; occurring between invariant chain-DR3 and antigenic peptide-DR3 complexes. The structure shows that the CLIP fragment binds to DR3 in a way almost identical to that in which antigenic peptides bind class II histocompatibility glycoproteins. The structure is the substrate for the loading of antigenic peptides by an exchange process catalysed by DM.
PubMed ID
Search related article in PubMed
Keywords
MHC GLYCOPROTEIN; COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN)




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Ag-Ab Interaction of the1A6A between chain "C" and chain "A"



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Epitope found in chain   :C                                                                                           
Epitope Sequence:-PVSKMRMATPLLMQA
Epitope Position found in PDB File   :   87-101  (Highlighted in white spacefill model)
P V S K M R M A T P L L M Q A

Download PDB File Download Ag-Ab Interaction PDB File

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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.