1KJV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

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

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

Date :   05 Dec 01 (Deposition) - 18 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

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

Keywords :   Peptide-Mhc, Major Histocompatibility Complex, 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) Molecules 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 - MATURE ALPHA CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN (HEAVY CHAIN)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 1-276 PLUS C- TERMINAL HIS TAG
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	MHC CLASS I RT1-A1C HEAVY CHAIN

Molecule 2 - BETA-2-MICROGLOBULIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 21-119, NUMBERED 2-100
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 3 - PEPTIDE NPR
	Chains	:	P
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE WAS DESIGNED FROM BIOCHEMICAL STUDIES.
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:75 , ASP A:137 , PHE A:138 , ARG A:141 , HOH A:655 , HOH A:674 , HOH A:774	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	THR A:258 , ARG A:260 , SER A:271 , ARG A:273 , LYS B:44 , LYS B:45 , HOH B:549 , HOH B:569	BINDING SITE FOR RESIDUE SO4 B 502
3	AC3	SOFTWARE	ARG A:75 , ARG A:79 , ARG A:82 , HOH A:520	BINDING SITE FOR RESIDUE SO4 A 503
4	AC4	SOFTWARE	LYS B:41 , PHE B:70 , THR B:71 , TYR B:78	BINDING SITE FOR RESIDUE SO4 B 504

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 1KJV)

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.	B2MG_RAT	98-104	1	B:78-84

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:0-3	4
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
	(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:276
 aligned with Q95565_RAT | Q95565 from UniProtKB/TrEMBL  Length:345

    Alignment length:276
                                    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      
           Q95565_RAT     1 GSHSLRYFDIAVSRPGLGEPRYISVGYVDDTEFARYDSDAENRRYQPRARWMEREGPEYWERNTPIYKGKEQTFRVNLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYEQFAYDGRDYIALNEDLKTWTAADFAARISRNKLERDGFADLHRAYLEGECVESLRRYLELGKETLLRSDPPKAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEP 276
               SCOP domains d1kjva2 A:1-181 Class I MHC, alpha-1 and alpha-2 domains                                                                                                                             d1kjva1 A:182-276 Class I MHC, alpha-3 domain                                                   SCOP domains
               CATH domains 1kjvA01 A:1-181 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                          1kjvA02 A:182-272 Immunoglobulins                                                          ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeeeee.....eeeeee..ee.hhhhee...ee.....eeeeeeeee...hhh.eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kjv A   1 GSHSLRYFDIAVSRPGLGEPRYISVGYVDDTEFARYDSDAENRRYQPRARWMEREGPEYWERNTPIYKGKEQTFRVNLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYEQFAYDGRDYIALNEDLKTWTAADFAARISRNKLERDGFADLHRAYLEGECVESLRRYLELGKETLLRSDPPKAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEP 276
                                    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:100
 aligned with B2MG_RAT | P07151 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:100
                                    29        39        49        59        69        79        89        99       109       119
             B2MG_RAT    20 AIQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM 119
               SCOP domains d1kjvb_ B: beta2-microglobulin                                                                       SCOP domains
               CATH domains 1kjvB00 B:0-99 Immunoglobulins                                                                       CATH domains
               Pfam domains -----------C1-set-1kjvB01 B:11-92                                                            ------- Pfam domains
         Sec.struct. author ......eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee..... 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)
                 1kjv B   0 MIQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with UBQL1_RAT | Q9JJP9 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:9
            UBQL1_RAT   450 NPRAMQALL 458
               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
                 1kjv P   1 NPRAMQALL   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)

C1-set-1kjvB01

B:11-92

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q95565_RAT | Q95565)

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.

Chain P (UBQL1_RAT | Q9JJP9)

molecular function
	GO:0031593	polyubiquitin modification-dependent protein binding	Interacting selectively and non-covalently with a protein upon poly-ubiquitination of the target protein.
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
biological process
	GO:0035973	aggrephagy	Selective degradation of protein aggregates by macroautophagy.
	GO:0006914	autophagy	The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
	GO:0071456	cellular response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:1901340	negative regulation of store-operated calcium channel activity	Any process that stops, prevents or reduces the frequency, rate or extent of store-operated calcium channel activity.
	GO:1903071	positive regulation of ER-associated ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of ER-associated ubiquitin-dependent protein catabolic process.
	GO:0031398	positive regulation of protein ubiquitination	Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:1902175	regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	Any process that modulates the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
	GO:0031396	regulation of protein ubiquitination	Any process that modulates the frequency, rate or extent of the addition of ubiquitin groups to a protein.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
	GO:0016235	aggresome	An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
	GO:0005776	autophagosome	A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.
	GO:0000502	proteasome complex	A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.

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
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His B:31 - Pro B:32	[ RasMol ]
		Tyr A:209 - Pro A:210	[ 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
	1kjv
		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
	B2MG_RAT \| P07151
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q95565_RAT \| Q95565
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	UBQL1_RAT \| Q9JJP9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	B2MG_RAT \| P07151
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q95565_RAT \| Q95565
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	UBQL1_RAT \| Q9JJP9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	B2MG_RAT \| P07151	:	1ed3 1frt 1i1a 1kjm 2frt 3fru

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 3)

Pfam Domains (1, 1)

Gene Ontology (63, 71)

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