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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AUTOIMMUNE MHC CLASS II I-AU COMPLEXED WITH MYELIN BASIC PROTEIN 1-11 AT 2.2A
 
Authors :  X. L. He, C. Radu, E. S. Ward, K. C. Garcia
Date :  26 Sep 01  (Deposition) - 04 Mar 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Mhc Class Ii, I-Au, H-2U, Autoimmune Disease, Unique Register, Experimental Autoimmune Encephalomyelitis, Myelin Basic Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. L. He, C. Radu, J. Sidney, A. Sette, E. S. Ward, K. C. Garcia
Structural Snapshot Of Aberrant Antigen Presentation Linked To Autoimmunity: The Immunodominant Epitope Of Mbp Complexe With I-Au
Immunity V. 17 83 2002
PubMed-ID: 12150894  |  Reference-DOI: 10.1016/S1074-7613(02)00340-0

(-) Compounds

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-U ALPHA CHAIN
    ChainsA
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System Taxid7227
    FragmentEXTRACELLULAR ALPHA-1 AND ALPHA-2 DOMAINS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMHC CLASS II I-AU
 
Molecule 2 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-U BETA CHAIN
    ChainsB
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System Taxid7227
    FragmentEXTRACELLULAR BETA-1 AND BETA-2 DOMAINS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMHC CLASS II I-AU
 
Molecule 3 - MYELIN BASIC PROTEIN PEPTIDE WITH 8 RESIDUE LINKER PEPTIDE
    ChainsP
    EngineeredYES
    Fragment11 RESIDUE PEPTIDE WITH 8 RESIDUE LINKER PEPTIDE
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE MBP PORTION OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymMBP PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:77 , ASN A:78 , GLU B:52BINDING SITE FOR RESIDUE NDG A 501
2AC2SOFTWAREASN A:118 , GLU A:166 , HOH A:589BINDING SITE FOR RESIDUE NAG A 502
3AC3SOFTWAREASP A:4 , THR B:18 , ASN B:19 , GLN B:22 , HOH B:677BINDING SITE FOR RESIDUE NAG B 503

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:15 -Pro A:16
2Phe A:113 -Pro A:114
3Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K2D)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.HA2U_MOUSE159-165  1A:161-167
HB2U_MOUSE197-203  1B:171-177

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003559942aENSE00001421865chr18:74844774-74844536239MBP_HUMAN-00--
1.4ENST000003559944ENSE00002187900chr18:74817242-7481716776MBP_HUMAN1-17170--
1.8aENST000003559948aENSE00001400728chr18:74778341-7477825488MBP_HUMAN18-47300--
1.10eENST0000035599410eENSE00001432843chr18:74729224-74728788437MBP_HUMAN47-1921460--
1.13cENST0000035599413cENSE00001179369chr18:74702016-74701912105MBP_HUMAN193-227350--
1.14eENST0000035599414eENSE00001000086chr18:74700868-7470083336MBP_HUMAN228-239120--
1.14gENST0000035599414gENSE00001278460chr18:74700483-7470045133MBP_HUMAN240-250110--
1.14oENST0000035599414oENSE00001656901chr18:74696850-74696731120MBP_HUMAN251-290401P:-3-8 (gaps)18
1.15lENST0000035599415lENSE00001606913chr18:74692427-746907901638MBP_HUMAN291-304140--

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:182
 aligned with HA2U_MOUSE | P14438 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:182
                               1                                                                                                                                                                                  
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  
           HA2U_MOUSE     - ---DHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE 179
               SCOP domains d1k2da2 A:1-81 Class II MHC alpha chain, N-terminal domain                        d1k2da1 A:82-181 Class II MHC alpha chain, C-terminal domain                                         SCOP domains
               CATH domains --1k2dA01 A:3-81                                                                  1k2dA02 A:82-181 Immunoglobulins                                                                     CATH domains
               Pfam domains ---MHC_II_alpha-1k2dA02 A:4-84                                                       --------C1-set-1k2dA01 A:93-175                                                            ------ Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k2d A   1 IEADHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE 181
                                    9A        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179  
                                    9A                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with HB2U_MOUSE | P06344 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:185
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
           HB2U_MOUSE    32 RHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA 216
               SCOP domains d1k2db2 B:5-92 Class II MHC beta chain, N-terminal domain                              d1k2db1 B:93-190 Class II MHC beta chain, C-terminal domain                                        SCOP domains
               CATH domains 1k2dB01 B:5-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1k2dB02 B:93-190 Immunoglobulins                                                                   CATH domains
               Pfam domains ---------MHC_II_beta-1k2dB02 B:14-86                                             ----------------C1-set-1k2dB01 B:103-190                                                                 Pfam domains
         Sec.struct. author ..eeeeeeeeeee.......eeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k2d B   5 RHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA 190
                                    14        24        34        44        54        64|       76        85        95       105       115       125       135       145       155       165       175       185     
                                                                                      64|               84A                                                                                                          
                                                                                       67                                                                                                                            

Chain P from PDB  Type:PROTEIN  Length:12
 aligned with MBP_HUMAN | P02686 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:18
                                   264        
            MBP_HUMAN   255 QRPGFGYGGRASDYKSAH 272
               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 1 Exon 1.14o         Transcript 1
                 1k2d P  -3 SR-----GG-ASQYRPSQ   8
                             |     ||-|       
                            -2    -1| 1       
                                    0         

   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  (4, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 4)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Family: C1-set (338)
(-)
Clan: MHC (252)

(-) Gene Ontology  (37, 48)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HA2U_MOUSE | P14438)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    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 II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0048002    antigen processing and presentation of peptide antigen    The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
    GO:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    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:0045582    positive regulation of T cell differentiation    Any process that activates or increases the frequency, rate or extent of T cell differentiation.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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   (HB2U_MOUSE | P06344)
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:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    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.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    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.

Chain P   (MBP_HUMAN | P02686)
molecular function
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019911    structural constituent of myelin sheath    The action of a molecule that contributes to the structural integrity of the myelin sheath of a nerve.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0008366    axon ensheathment    Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    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:0061024    membrane organization    A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
    GO:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0050771    negative regulation of axonogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
    GO:0070542    response to fatty acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:0046689    response to mercury ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
    GO:0032570    response to progesterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0034612    response to tumor necrosis factor    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0043218    compact myelin    The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs.
    GO:0033269    internode region of axon    An axon part that is located between the nodes of Ranvier and surrounded by compact myelin sheath.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HA2U_MOUSE | P144381u3h 2p24 2pxy 2z31
        HB2U_MOUSE | P063441u3h 2p24 2pxy 2z31
        MBP_HUMAN | P026861bx2 1fv1 1hqr 1qcl 1ymm 1zgl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1K2D)