1K8I - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE H2-DM

Authors :   D. H. Fremont, F. Crawford, P. Marrack, W. Hendrickson, J. Kappler

Date :   24 Oct 01 (Deposition) - 05 Dec 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Fremont, F. Crawford, P. Marrack, W. A. Hendrickson, J. Kappler
Crystal Structure Of Mouse H2-M.
Immunity V. 9 385 1998
PubMed-ID: 9768758 | Reference-DOI: 10.1016/S1074-7613(00)80621-4

Molecule 1 - MHC CLASS II H2-M ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH-FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	H2-DM
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - MHC CLASS II H2-M BETA 2 CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH-FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	H2-DM
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:11 , ASN A:12 , GLN B:19	BINDING SITE FOR RESIDUE NAG A 192
2	AC2	SOFTWARE	GLY A:141 , ASN A:162	BINDING SITE FOR RESIDUE NAG A 193

Asymmetric/Biological Unit

No.	Residues
1	A:21	-	A:76
2	A:118	-	A:173
3	B:10	-	B:78
4	B:24	-	B:34
5	B:116	-	B:173

Asymmetric/Biological Unit

No.	Residues
1	Phe A:124	-	Pro A:125
2	Tyr B:122	-	Pro B:123

(no "SAP(SNP)/Variant" information available for 1K8I)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	DMA_MOUSE	200-206	1	A:171-177

(no "Exon" information available for 1K8I)

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:181
 aligned with DMA_MOUSE | P28078 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:181
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
            DMA_MOUSE    40 QNHTFRHTLFCQDGIPNIGLSETYDEDELFSFDFSQNTRVPRLPDFAEWAQGQGDASAIAFGKSFCEMLMREVSPKLEGQIPVSRGLSVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPVEGASPTSISAVDGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQ 220
               SCOP domains d1k8ia2 A:11-92 Class II MHC alpha chain, N-terminal domain                       d1k8ia1 A:93-191 Class II MHC alpha chain, C-terminal domain                                        SCOP domains
               CATH domains 1k8iA01 A:11-87                                                              1k8iA02 A:88-191 Immunoglobulins                                                                         CATH domains
               Pfam domains -MHC_II_alpha-1k8iA02 A:12-95                                                        --------C1-set-1k8iA01 A:104-183                                                        -------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeeee..eeeeeee....eeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee....eeeeeee..eee......eeeee...eeeeeeeeee.......eeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8i A  11 QNHTFRHTLFCQDGIPNIGLSETYDEDELFSFDFSQNTRVPRLPDFAEWAQGQGDASAIAFDKSFCEMLMREVSPKLEGQIPVSRGLPVAEVFTLKPLEFGKPNTLVCFISNLFPPTLTVNWQLHSAPVEGASPTSISAVDGLTFQAFSYLNFTPEPFDLYSCTVTHEIDRYTAIAYWVPQ 191
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with Q31099_MOUSE | Q31099 from UniProtKB/TrEMBL  Length:261

    Alignment length:190
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
         Q31099_MOUSE    20 GFVAHVESTCVLNDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFWDVLTHRTRAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 209
               SCOP domains d1k8ib2 B:1-94 Class II MHC beta chain, N-terminal domain                                     d1k8ib1 B:95-190 Class II MHC beta chain, C-terminal domain                                      SCOP domains
               CATH domains 1k8iB01 B:1-91 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1        1k8iB02 B:92-190 Immunoglobulins                                                                    CATH domains
               Pfam domains -------MHC_II_beta-1k8iB02 B:8-87                                                      --------------C1-set-1k8iB01 B:102-185                                                            ----- Pfam domains
         Sec.struct. author ..eeeeeeeeeee....eeee..eeee.....eeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee........eeeeeeeeee....eeeeeee..ee...........ee.....eeeeeeeee.......eeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k8i B   1 GFVAHVESTCVLNDAGTPQDFTYCVSFNKDLLACWDPDVGKIVPCEFGVLSRLAEIISNILNEQESLIHRLQNGLQDCATHTQPFWDVLTHRTRAPSVRVAQTTPFNTREPVMLACYVWGFYPADVTITWMKNGQLVPSHSNKEKTAQPNGDWTYQTVSYLALTPSYGDVYTCVVQHSGTSEPIRGDWTP 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Homologous Superfamily: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

House mouse (Mus musculus) (25)

1a	1k8iB01	B:1-91
1b	1k8iA01	A:11-87

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1k8iB02	B:92-190
2b	1k8iA02	A:88-191

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

1a	C1-set-1k8iA01	A:104-183
1b	C1-set-1k8iB01	B:102-185

Clan: MHC (252)

Family: MHC_II_alpha (42)

Mus musculus (Mouse) (16)

MHC_II_alpha-1k8iA02

A:12-95

Family: MHC_II_beta (39)

Mus musculus (Mouse) (14)

MHC_II_beta-1k8iB02

B:8-87

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DMA_MOUSE | P28078)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	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: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:0051085	chaperone mediated protein folding requiring cofactor	The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
	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:0016064	immunoglobulin mediated immune response	An immune response mediated by immunoglobulins, whether cell-bound or in solution.
	GO:0048839	inner ear development	The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
	GO:0002503	peptide antigen assembly with MHC class II protein complex	The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
	GO:0045582	positive regulation of T cell differentiation	Any process that activates or increases the frequency, rate or extent of T cell differentiation.
	GO:0002636	positive regulation of germinal center formation	Any process that activates or increases the frequency, rate, or extent of germinal center formation.
	GO:0002922	positive regulation of humoral immune response	Any process that activates or increases the frequency, rate, or extent of a humoral immune response.
	GO:0050778	positive regulation of immune response	Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0045059	positive thymic T cell selection	The process of sparing immature T cells in the thymus which react with self-MHC protein complexes with low affinity levels from apoptotic death.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	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:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.

Chain B (Q31099_MOUSE | Q31099)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	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: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:0051085	chaperone mediated protein folding requiring cofactor	The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
	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:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	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:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:124 - Pro A:125	[ RasMol ]
		Tyr B:122 - Pro B:123	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1k8i
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DMA_MOUSE \| P28078
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q31099_MOUSE \| Q31099
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DMA_MOUSE \| P28078
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q31099_MOUSE \| Q31099
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1K8I)

(no "Related Entries Specified in the PDB File" available for 1K8I)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (2, 4)

Pfam Domains (3, 4)

Gene Ontology (31, 47)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File