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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MOLECULAR DYNAMICS SIMULATION OF MHC-PEPTIDE COMPLEXES AS A TOOL FOR PREDICTING POTENTIAL TCELL EPITOPES
 
Authors :  D. Rognan, L. Scapozza, G. Folkers, A. Daser
Date :  19 Jul 94  (Deposition) - 30 Sep 94  (Release) - 30 Sep 94  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Histocompatibility Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Rognan, L. Scapozza, G. Folkers, A. Daser
Molecular Dynamics Simulation Of Mhc-Peptide Complexes As A Tool For Predicting Potential T Cell Epitopes.
Biochemistry V. 33 11476 1994
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-B*2705)
    Chains: A
    Engineered: YES
    Expression System Vector Type: BACTERIAL
    Gene: POTENTIAL
    Organism Scientific: HOMO SAPIENS
 
Molecule 2 - 
    Chains: B
    Engineered: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1NME1Mod. Amino AcidMETHYLAMINE

(-) Sites  (0, 0)

(no "Site" information available for 1ROH)

(-) SS Bonds  (1, 1)

Theoretical Model
No.Residues
1A:101 -A:164

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ROH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Theoretical Model (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_056341A65T1B27_HUMANPolymorphism1050529AA41T
02UniProtVAR_016379Y83H1B27_HUMANPolymorphism  ---AY59H
03UniProtVAR_016380D101N1B27_HUMANPolymorphism  ---AD77N
04UniProtVAR_016381D101S1B27_HUMANPolymorphism  ---AD77S
05UniProtVAR_016383T104N1B27_HUMANPolymorphism  ---AT80N
06UniProtVAR_016385N121S1B27_HUMANPolymorphism  ---AN97S
07UniProtVAR_016387H138D1B27_HUMANPolymorphism  ---AH114D
08UniProtVAR_016388D140H1B27_HUMANPolymorphism  ---AD116H
09UniProtVAR_016389D140Y1B27_HUMANPolymorphism  ---AD116Y
10UniProtVAR_016390S155R1B27_HUMANPolymorphism  ---AS131R
11UniProtVAR_016391V176E1B27_HUMANPolymorphism  ---AV152E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ROH)

(-) Exons   (0, 0)

(no "Exon" information available for 1ROH)

(-) Sequences/Alignments

Theoretical Model
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:183
 aligned with 1B27_HUMAN | P03989 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:183
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204   
           1B27_HUMAN    25 GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYWDRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQRAD 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..........eeeeeee..eeee...............hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeeeee.....eeeeeeeeee..eeeeee......eee..hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhh......... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------T-----------------H-----------------N--N----------------S----------------D-H--------------R--------------------E------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------S--------------------------------------Y------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1roh A   1 GSHSMRYFHTSVSRPGRGEPRFITVGYVDDTLFVRFDSDAASPREEPRAPWIEQEGPEYWDRETQICKAKAQTDREDLRTLLRYYNQSEAGSHTLQNMYGCDVGPDGRLLRGYHQDAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGECVEWLRRYLENGKETLQRAx 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  |
                                                                                                                                                                                                                183-NME


Chain B from PDB  Type:PROTEIN  Length:9
 aligned with DNAK_CLOAB | P30721 from UniProtKB/Swiss-Prot  Length:615

    Alignment length:9
           DNAK_CLOAB   232 QRLKEAAEK 240
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1roh B   1 QRLKEAAEK   9
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1ROH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ROH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ROH)

(-) Gene Ontology  (31, 31)

Theoretical Model(hide GO term definitions)
Chain A   (1B27_HUMAN | P03989)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002486    antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent    The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-independent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following transport from the cytosol via a TAP-independent pathway. Class I here refers to classical class I molecules.
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0002480    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a pathway not requiring TAP (transporter associated with antigen processing). The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell. Class I here refers to classical class I molecules.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0060337    type I interferon signaling pathway    A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0071556    integral component of lumenal side of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (DNAK_CLOAB | P30721)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        1B27_HUMAN | P03989: 1hsa 1jgd 1jge 1k5n 1of2 1ogt 1rog 1roi 1roj 1rok 1rol 1uxs 1uxw 1w0v 1w0w 2a83 2bsr 2bss 2bst 3b3i 3b6s 3bp4 3bp7 3czf 3d18 3dtx 3hcv 3lv3 4g8g 4g8i 4g9d 4g9f 5def 5deg 5ib1 5ib2 5ib3 5ib4 5ib5

(-) Related Entries Specified in the PDB File

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