1QO3 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   COMPLEX BETWEEN NK CELL RECEPTOR LY49A AND ITS MHC CLASS I LIGAND H-2DD

Authors :   J. Tormo, R. A. Mariuzza

Date :   01 Nov 99 (Deposition) - 02 Jan 00 (Release) - 15 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,P
Biol. Unit 1: A (1x),B (1x),C (1x),D (1x),P (1x)
Biol. Unit 2: A (1x),B (1x),C (1x),D (1x),P (1x)

Keywords :   Receptor/Immune System, Complex (Nk Receptor/Mhc Class I), Nk Cell, Inhibitory Receptor, Mhc-I, C-Type Lectin-Like, Histocompatibility, B2M, Ly49, Ly-49 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Tormo, K. Natarajan, D. H. Margulies, R. A. Mariuzza
Crystal Structure Of A Lectin-Like Natural Killer Cell Receptor Bound To Its Mhc Class I Ligand
Nature V. 402 623 1999
PubMed-ID: 10604468 | Reference-DOI: 10.1038/45170
(for further references see the PDB file header)

Molecule 1 - MHC CLASS I H-2DD HEAVY CHAIN
	Cell	:	MOST NUCLEATED CELLS
	Cellular Location	:	CELL SURFACE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	INCLUSION BODY
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	EXTRACELLULAR DOMAIN
	Gene	:	H-2D
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C
	Synonym	:	H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-D ALPHA CHAIN, (H-2D(D))

Molecule 2 - BETA-2-MICROGLOBULIN
	Cell	:	MOST NUCLEATED CELLS
	Cellular Location	:	CELL SURFACE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	INCLUSION BODY
	Expression System Plasmid	:	PET21D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C57BL/6
	Synonym	:	B2M

Molecule 3 - HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
	Chains	:	P
	Fragment	:	RESIDUES 318-327
	Mutation	:	YES
	Organism Common	:	HIV
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS
	Organism Taxid	:	12721
	Strain	:	HIV IIIB
	Synthetic	:	YES

Molecule 4 - LY49A
	Cell	:	NATURAL KILLER CELLS SOME T CELLS
	Cellular Location	:	CELL SURFACE
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	INCLUSION BODY
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	C-TYPE LECTIN-LIKE DOMAIN
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C57BL/6
	Synonym	:	NK-CELL SURFACE GLYCOPROTEIN YE1/48, T LYMPHOCYTE ANTIGEN A1, LY49-A ANTIGEN, LY49A

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	P
Biological Unit 1 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	P (1x)
Biological Unit 2 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	P (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:170 , HOH C:2064	BINDING SITE FOR RESIDUE EDO A1276
2	AC2	SOFTWARE	TRP A:114 , TRP A:147 , ALA A:152 , ASP A:156 , HOH A:2157 , ARG P:5 , VAL P:8	BINDING SITE FOR RESIDUE EDO A1277
3	AC3	SOFTWARE	HIS A:188 , TRP A:204 , PRO B:14 , HOH B:2017	BINDING SITE FOR RESIDUE EDO A1278

Asymmetric Unit

No.	Residues
1	A:101	-	A:164
2	A:203	-	A:259
3	B:25	-	B:80
4	C:145	-	C:150
5	C:163	-	C:251
6	C:167	-	C:253
7	C:232	-	C:245
8	D:145	-	D:150
9	D:163	-	D:251
10	D:167	-	D:253
11	D:232	-	D:245

Asymmetric Unit

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

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_B2MG_MOUSE_002 *	H	54	Q	B2MG_MOUSE	---	---	B	H	34	Q
2	UniProt	VAR_B2MG_MOUSE_003 *	K	64	E	B2MG_MOUSE	---	---	B	K	44	E
3	UniProt	VAR_B2MG_MOUSE_004 *	R	101	T	B2MG_MOUSE	---	---	B	R	81	T
4	UniProt	VAR_B2MG_MOUSE_005 *	A	105	D	B2MG_MOUSE	---	---	B	A	85	D
5	UniProt	VAR_B2MG_MOUSE_006 *	A	105	V	B2MG_MOUSE	---	---	B	A	85	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_B2MG_MOUSE_002 *	H	54	Q	B2MG_MOUSE	---	---	B	H	34	Q
2	UniProt	VAR_B2MG_MOUSE_003 *	K	64	E	B2MG_MOUSE	---	---	B	K	44	E
3	UniProt	VAR_B2MG_MOUSE_004 *	R	101	T	B2MG_MOUSE	---	---	B	R	81	T
4	UniProt	VAR_B2MG_MOUSE_005 *	A	105	D	B2MG_MOUSE	---	---	B	A	85	D
5	UniProt	VAR_B2MG_MOUSE_006 *	A	105	V	B2MG_MOUSE	---	---	B	A	85	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_B2MG_MOUSE_002 *	H	54	Q	B2MG_MOUSE	---	---	B	H	34	Q
2	UniProt	VAR_B2MG_MOUSE_003 *	K	64	E	B2MG_MOUSE	---	---	B	K	44	E
3	UniProt	VAR_B2MG_MOUSE_004 *	R	101	T	B2MG_MOUSE	---	---	B	R	81	T
4	UniProt	VAR_B2MG_MOUSE_005 *	A	105	D	B2MG_MOUSE	---	---	B	A	85	D
5	UniProt	VAR_B2MG_MOUSE_006 *	A	105	V	B2MG_MOUSE	---	---	B	A	85	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MOUSE	98-104	1	B:78-84
1	IG_MHC	PS00290		HA12_MOUSE	281-287	1	A:257-263
2	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	KLRA1_MOUSE	146-254	2	C:146-254 D:146-254

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MOUSE	98-104	1	B:78-84
1	IG_MHC	PS00290		HA12_MOUSE	281-287	1	A:257-263
2	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	KLRA1_MOUSE	146-254	2	C:146-254 D:146-254

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	B2MG_MOUSE	98-104	1	B:78-84
1	IG_MHC	PS00290		HA12_MOUSE	281-287	1	A:257-263
2	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	KLRA1_MOUSE	146-254	2	C:146-254 D:146-254

(no "Exon" information available for 1QO3)

Asymmetric 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:274
 aligned with HA12_MOUSE | P01900 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:274
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    
           HA12_MOUSE    26 SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWG 299
               SCOP domains d1qo3a2 A:2-181 Class I MHC, alpha-1 and alpha-2 domains                                                                                                                            d1qo3a1 A:182-275 Class I MHC, alpha-3 domain                                                  SCOP domains
               CATH domains 1qo3A01 A:2-181 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                         1qo3A02 A:182-272 Immunoglobulins                                                          --- CATH domains
               Pfam domains MHC_I-1qo3A02 A:2-179                                                                                                                                                             --------C1-set-1qo3A01 A:188-271                                                            ---- Pfam domains
         Sec.struct. author .eeeeeeeeee........eeeeeeee..eeeeeee...........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeee.......eeeeee.......................eeeeeee...hhh.eeeeee.......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo3 A   2 SHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWG 275
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with B2MG_MOUSE | P01887 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:100
                                    29        39        49        59        69        79        89        99       109       119
           B2MG_MOUSE    20 AIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM 119
               SCOP domains d1qo3b_ B: beta2-microglobulin                                                                       SCOP domains
               CATH domains 1qo3B00 B:0-99 Immunoglobulins                                                                       CATH domains
               Pfam domains -----------C1-set-1qo3B01 B:11-92                                                            ------- Pfam domains
         Sec.struct. author ......eeeeee........eeeeeeeee.......eeeeee......................eeeeeeee......eeeeee.......eeee..... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------Q---------E------------------------------------T---D-------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------V-------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1qo3 B   0 MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with KLRA1_MOUSE | P20937 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:133
                                   135       145       155       165       175       185       195       205       215       225       235       245       255   
          KLRA1_MOUSE   126 KTVLDSLQHTGRGDKVYWFCYGMKCYYFVMDRKTWSGCKQACQSSSLSLLKIDDEDELKFLQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTGKYNIRDGGCMLLSKTRLDNGNCDQVFICICGKRLD 258
               SCOP domains d1qo3c_ C     : NK cell receptor                                                                                                      SCOP domains
               CATH domains 1qo3C00 C     :126-258 Mannose-Binding Protein A, subunit A                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........-----.eeeeee..eeeeee....hhhhhhhhhhhh........hhhhhhhhhhhh........eeeehhhheeee...............hhhhh.eeee....eeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------C_TYPE_LECTIN_2  PDB: C:146-254 UniProt: 146-254                                                             ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo3 C 126 STVLDSLQH-----KVYWFCYGMKCYYFVMDRKTWSGCKQTCQSSSLSLLKIDDEDELKFLQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTRKYNIRDGGCMLLSKTRLDNGNCDQVFICICGKRLD 258
                                    |-    |  145       155       165       175       185       195       205       215       225       235       245       255   
                                  134   140

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with KLRA1_MOUSE | P20937 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:121
                                   148       158       168       178       188       198       208       218       228       238       248       258 
          KLRA1_MOUSE   139 DKVYWFCYGMKCYYFVMDRKTWSGCKQACQSSSLSLLKIDDEDELKFLQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTGKYNIRDGGCMLLSKTRLDNGNCDQVFICICGKRLDK 259
               SCOP domains d1qo3d_ D: NK cell receptor                                                                                               SCOP domains
               CATH domains 1qo3D00 D:139-259 Mannose-Binding Protein A, subunit A                                                                    CATH domains
           Pfam domains (1) Ly49-1qo3D03   --Lectin_C-1qo3D01 D:156-255                                                                          ---- Pfam domains (1)
           Pfam domains (2) Ly49-1qo3D04   --Lectin_C-1qo3D02 D:156-255                                                                          ---- Pfam domains (2)
         Sec.struct. author ..eeeeee..eeeeee....hhhhhhhhhhhh........hhhhhhhhhhhh........eeee....eeee..........hhhhhhhhhh.eeee....eeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------C_TYPE_LECTIN_2  PDB: D:146-254 UniProt: 146-254                                                             ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qo3 D 139 DKVYWFCYGMKCYYFVMDRKTWSGCKQTCQSSSLSLLKIDDEDELKFLQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTRKYNIRDGGCMLLSKTRLDNGNCDQVFICICGKRLDK 259
                                   148       158       168       178       188       198       208       218       228       238       248       258

Chain P from PDB  Type:PROTEIN  Length:10
 aligned with ENV_HV1B8 | P04582 from UniProtKB/Swiss-Prot  Length:851

    Alignment length:10
                                   320
            ENV_HV1B8   311 RGPGRAFVTI 320
               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
                 1qo3 P   1 RGPGRAFVTI  10
                                    10

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 Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C_Lectin (98)

Family: Lectin_C (85)

Mus musculus (Mouse) (4)

1a	Lectin_C-1qo3D01	D:156-255
1b	Lectin_C-1qo3D02	D:156-255

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

2a	C1-set-1qo3B01	B:11-92
2b	C1-set-1qo3A01	A:188-271

Clan: MHC (252)

Family: MHC_I (210)

Mus musculus (Mouse) (60)

MHC_I-1qo3A02

A:2-179

Clan: no clan defined [family: Ly49] (2)

Family: Ly49 (2)

Mus musculus (Mouse) (2)

4a	Ly49-1qo3D03	D:139-153
4b	Ly49-1qo3D04	D:139-153

Asymmetric Unit(hide GO term definitions)

Chain A (HA12_MOUSE | P01900)

molecular function
	GO:0042608	T cell receptor binding	Interacting selectively and non-covalently with a T cell receptor, the antigen-recognizing receptor on the surface of T cells.
	GO:0046977	TAP binding	Interacting selectively and non-covalently with TAP protein, transporter associated with antigen processing protein. TAP protein is a heterodimeric peptide transporter consisting of the subunits TAP1 and TAP2.
	GO:0030881	beta-2-microglobulin binding	Interacting selectively and non-covalently with beta-2-microglobulin.
	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).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
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:0002485	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules.
	GO:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO: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.
	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:0001916	positive regulation of T cell mediated cytotoxicity	Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
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:0005797	Golgi medial cisterna	The middle Golgi cisterna (or cisternae).
	GO:0042612	MHC class I protein complex	A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO: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:0070971	endoplasmic reticulum exit site	An endoplasmic reticulum part at which COPII-coated vesicles are produced.
	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:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (B2MG_MOUSE | P01887)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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:0002479	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
	GO: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:0006968	cellular defense response	A defense response that is mediated by cells.
	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:0030670	phagocytic vesicle membrane	The lipid bilayer surrounding a phagocytic vesicle.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain C,D (KLRA1_MOUSE | P20937)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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: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 (ENV_HV1B8 | P04582)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

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	1qo3
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	KLRA1_MOUSE \| P20937
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(no "Related Entries Specified in the PDB File" available for 1QO3)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (11, 11)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (5, 5)

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Exons (0, 0)

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