1KJM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TAP-A-ASSOCIATED RAT MHC CLASS I MOLECULE

Authors :   M. G. Rudolph, J. Stevens, J. A. Speir, J. Trowsdale, G. W. Butcher, E. Jo I. A. Wilson

Date :   04 Dec 01 (Deposition) - 18 Dec 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Peptide-Mhc Complex, Heterodimer, Extracellular Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Rudolph, J. Stevens, J. A. Speir, J. Trowsdale, G. W. Butcher, E. Joly, I. A. Wilson
Crystal Structures Of Two Rat Mhc Class Ia (Rt1-A) Molecule That Are Associated Differentially With Peptide Transporter Alleles Tap-A And Tap-B.
J. Mol. Biol. V. 324 975 2002
PubMed-ID: 12470953 | Reference-DOI: 10.1016/S0022-2836(02)01095-1
(for further references see the PDB file header)

Molecule 1 - RT1 CLASS I HISTOCOMPATIBILITY ANTIGEN, AA ALPHA CHAIN, HEAVY CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 25-300, NUMBERED 1-276, PLUS C-TERMINAL HIS TAG
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	MHC CLASS I RT1-AA HEAVY CHAIN

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 21-119, NUMBERED 1-99
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 3 - B6 PEPTIDE
	Chains	:	P
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE WAS DERIVED FROM BIOCHEMICAL BINDING DATA.
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:86 , LYS A:131 , ARG A:157 , HOH A:329 , HOH A:362	BINDING SITE FOR RESIDUE SO4 A 286

Asymmetric/Biological Unit

No.	Residues
1	A:101	-	A:164
2	A:203	-	A:259
3	B:25	-	B:80

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:209	-	Pro A:210
2	His B:31	-	Pro B:32

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_RAT	98-104	1	B:78-84
1	IG_MHC	PS00290		HA12_RAT	281-287	1	A:257-263

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000023017	1	ENSRNOE00000164042	chr3:108927919-108927992	74	B2MG_RAT	1-23	23	1	B:1-3	3
1.2	ENSRNOT00000023017	2	ENSRNOE00000164162	chr3:108930763-108931041	279	B2MG_RAT	23-116	94	1	B:3-96	94
1.3	ENSRNOT00000023017	3	ENSRNOE00000164268	chr3:108931555-108931583	29	B2MG_RAT	116-119	4	1	B:96-99	4
1.4	ENSRNOT00000023017	4	ENSRNOE00000164313	chr3:108932497-108932718	222	B2MG_RAT	-	0	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:277
 aligned with HA12_RAT | P16391 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:277
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       
             HA12_RAT    25 GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYWEQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDGRDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLLRSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEPS 301
               SCOP domains d1kjma2 A:1-181 Class I MHC, alpha-1 and alpha-2 domains                                                                                                                             d1kjma1 A:182-277 Class I MHC, alpha-3 domain                                                    SCOP domains
               CATH domains 1kjmA01 A:1-181 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                          1kjmA02 A:182-272 Immunoglobulins                                                          ----- CATH domains
               Pfam domains MHC_I-1kjmA02 A:1-179                                                                                                                                                              ------C1-set-1kjmA01 A:186-271                                                              ------ Pfam domains
         Sec.struct. author .eeeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee....eeeeeeeeee..eeeeee......eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee...hhh.eeeeee.......eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kjm A   1 GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYWEQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDGRDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLLRSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEPL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with B2MG_RAT | P07151 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:99
                                    30        40        50        60        70        80        90       100       110         
             B2MG_RAT    21 IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM 119
               SCOP domains d1kjmb_ B: beta2-microglobulin                                                                      SCOP domains
               CATH domains 1kjmB00 B:1-99 Immunoglobulins                                                                      CATH domains
               Pfam domains ----------C1-set-1kjmB01 B:11-92                                                            ------- Pfam domains
         Sec.struct. author ........eee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee.......eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------1.3  Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: B:3-96 UniProt: 23-116                                                         --- Transcript 1 (2)
                 1kjm B   1 IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM  99
                                    10        20        30        40        50        60        70        80        90

Chain P from PDB  Type:PROTEIN  Length:9
                                         
               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
                 1kjm P   1 AQFSASASR   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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Rattus norvegicus (Rat) (3)

1a	C1-set-1kjmB01	B:11-92
1b	C1-set-1kjmA01	A:186-271

Clan: MHC (252)

Family: MHC_I (210)

Rattus norvegicus (Rat) (1)

MHC_I-1kjmA02

A:1-179

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HA12_RAT | P16391)

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: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: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: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: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 B (B2MG_RAT | P07151)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0033077	T cell differentiation in thymus	The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
	GO:0019731	antibacterial humoral response	An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
	GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	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. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.
	GO:0002481	antigen processing and presentation of exogenous protein antigen via MHC class Ib, 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 Ib 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 Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
	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:0071281	cellular response to iron ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0050829	defense response to Gram-negative bacterium	Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
	GO:0050830	defense response to Gram-positive bacterium	Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
	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:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	GO:0010977	negative regulation of neuron projection development	Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:1900121	negative regulation of receptor binding	Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
	GO:0002726	positive regulation of T cell cytokine production	Any process that activates or increases the frequency, rate, or extent of T cell cytokine production.
	GO:0001916	positive regulation of T cell mediated cytotoxicity	Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
	GO:1904434	positive regulation of ferrous iron binding	Any process that activates or increases the frequency, rate or extent of ferrous iron binding.
	GO:0032092	positive regulation of protein binding	Any process that activates or increases the frequency, rate or extent of protein binding.
	GO:1900122	positive regulation of receptor binding	Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
	GO:0048260	positive regulation of receptor-mediated endocytosis	Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
	GO:1904437	positive regulation of transferrin receptor binding	Any process that activates or increases the frequency, rate or extent of transferrin receptor binding.
	GO:0042026	protein refolding	The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
	GO:0003254	regulation of membrane depolarization	Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
	GO:0046686	response to cadmium 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 cadmium (Cd) ion stimulus.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0002237	response to molecule of bacterial origin	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
	GO:0001895	retina homeostasis	A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
	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:1990712	HFE-transferrin receptor complex	A protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	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.

Asymmetric/Biological Unit
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	1kjm
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	B2MG_RAT \| P07151	:	1ed3 1frt 1i1a 1kjv 2frt 3fru
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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (3, 3)

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