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Title :   STRUCTURE OF THE MHC CLASS I HOMOLOG MIC-A, A GAMMADELTA T CELL LIGAND

Authors :   P. Li, S. Willie, S. Bauer, D. Morris, T. Spies, R. Strong

Date :   11 Dec 98 (Deposition) - 09 Jul 99 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A

Keywords :   Hc I Homolog, Human Mica, Mica, Immunology, Mhc, Gamma-Delta-Tcr, Glycoprotein, Signa Immunoglobulin Fold, T-Cell, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Li, S. T. Willie, S. Bauer, D. L. Morris, T. Spies, R. K. Strong
Crystal Structure Of The Mhc Class I Homolog Mic-A, A Gammadelta T Cell Ligand.
Immunity V. 10 577 1999
PubMed-ID: 10367903 | Reference-DOI: 10.1016/S1074-7613(00)80057-6
(for further references see the PDB file header)

Molecule 1 - MHC CLASS I HOMOLOG MIC-A
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HI5
	Expression System Common	:	CABBAGE LOOPER
	Expression System Gene	:	MICA-001
	Expression System Taxid	:	7111
	Expression System Vector	:	BACULOVIRUS
	Fragment	:	EXTRACELLULAR DOMAIN, RESIDUES 1 - 274
	Gene	:	MICA-001
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MICA, MIC, PERB11

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:8 , THR A:10 , GLU A:25 , ILE A:93 , ASP A:236 , NAG A:302	BINDING SITE FOR RESIDUE NAG A 301
2	AC2	SOFTWARE	NAG A:301 , HOH A:307 , HOH A:323	BINDING SITE FOR RESIDUE NAG A 302

Asymmetric/Biological Unit

No.	Residues
1	A:36	-	A:41
2	A:96	-	A:164
3	A:202	-	A:259

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:208	-	Pro A:209

Asymmetric/Biological Unit (29, 29)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_043625	R	29	P	MICA_HUMAN	Polymorphism	9380254	A	R	6	P
02	UniProt	VAR_043626	W	37	G	MICA_HUMAN	Polymorphism	1063630	A	W	14	G
03	UniProt	VAR_043627	T	47	A	MICA_HUMAN	Polymorphism	1051785	A	T	24	A
04	UniProt	VAR_043628	V	49	G	MICA_HUMAN	Polymorphism	17200158	A	V	26	G
05	UniProt	VAR_043629	C	59	Y	MICA_HUMAN	Polymorphism	1051786	A	C	36	Y
06	UniProt	VAR_043630	Q	114	R	MICA_HUMAN	Polymorphism	41558312	A	Q	91	R
07	UniProt	VAR_043631	R	128	K	MICA_HUMAN	Polymorphism	41557113	A	R	105	K
08	UniProt	VAR_043632	G	137	R	MICA_HUMAN	Polymorphism	41556715	A	G	114	R
09	UniProt	VAR_043633	L	145	V	MICA_HUMAN	Polymorphism	1051790	A	L	122	V
10	UniProt	VAR_043634	T	147	S	MICA_HUMAN	Polymorphism	41539919	A	T	124	S
11	UniProt	VAR_043635	K	148	E	MICA_HUMAN	Polymorphism	1051791	A	K	125	E
12	UniProt	VAR_043636	M	152	V	MICA_HUMAN	Polymorphism	1051792	A	M	129	V
13	UniProt	VAR_043637	V	165	I	MICA_HUMAN	Polymorphism	3819269	A	V	142	I
14	UniProt	VAR_043638	M	174	V	MICA_HUMAN	Polymorphism	41560824	A	M	151	V
15	UniProt	VAR_043640	K	196	E	MICA_HUMAN	Polymorphism	1051794	A	K	173	E
16	UniProt	VAR_043641	G	198	S	MICA_HUMAN	Polymorphism	1131896	A	G	175	S
17	UniProt	VAR_043642	V	199	I	MICA_HUMAN	Polymorphism	41549718	A	V	176	I
18	UniProt	VAR_043643	T	204	R	MICA_HUMAN	Polymorphism	1131897	A	T	181	R
19	UniProt	VAR_043644	G	229	S	MICA_HUMAN	Polymorphism	1131898	A	G	206	S
20	UniProt	VAR_043645	Y	231	C	MICA_HUMAN	Polymorphism	41546915	A	Y	208	C
21	UniProt	VAR_043646	W	233	R	MICA_HUMAN	Polymorphism	1051798	A	W	210	R
22	UniProt	VAR_043647	T	236	I	MICA_HUMAN	Polymorphism	1140700	A	T	213	I
23	UniProt	VAR_043648	S	238	T	MICA_HUMAN	Polymorphism	1051799	A	S	215	T
24	UniProt	VAR_043649	V	244	L	MICA_HUMAN	Polymorphism	41540613	A	V	221	L
25	UniProt	VAR_043869	W	253	S	MICA_HUMAN	Polymorphism	72558175	A	W	230	S
26	UniProt	VAR_043650	Q	274	R	MICA_HUMAN	Polymorphism	1063635	A	Q	251	R
27	UniProt	VAR_043651	R	279	S	MICA_HUMAN	Polymorphism	41557614	A	R	256	S
28	UniProt	VAR_043652	S	291	G	MICA_HUMAN	Polymorphism	61759927	A	S	268	G
29	UniProt	VAR_043653	P	294	A	MICA_HUMAN	Polymorphism	41553616	A	P	271	A

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

(no "PROSITE Motif" information available for 1B3J)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000400325	1c	ENSE00001802778	HSCHR6_MHC_QBL:31358575-31358589	15	MICA_HUMAN	-	0	0	-	-
1.2	ENST00000400325	2	ENSE00001765771	HSCHR6_MHC_QBL:31359983-31360182	200	MICA_HUMAN	-	0	0	-	-
1.3a	ENST00000400325	3a	ENSE00001778375	HSCHR6_MHC_QBL:31361271-31361528	258	MICA_HUMAN	1-24	24	1	A:1-1	1
1.4	ENST00000400325	4	ENSE00001751066	HSCHR6_MHC_QBL:31368470-31368724	255	MICA_HUMAN	24-109	86	1	A:1-86	86
1.5b	ENST00000400325	5b	ENSE00001651377	HSCHR6_MHC_QBL:31368999-31369286	288	MICA_HUMAN	109-205	97	1	A:86-182 (gaps)	97
1.6	ENST00000400325	6	ENSE00001666138	HSCHR6_MHC_QBL:31369874-31370152	279	MICA_HUMAN	205-298	94	1	A:182-274	93
1.7	ENST00000400325	7	ENSE00001497291	HSCHR6_MHC_QBL:31370253-31370384	132	MICA_HUMAN	298-342	45	0	-	-
1.8a	ENST00000400325	8a	ENSE00001672548	HSCHR6_MHC_QBL:31372936-31373183	248	MICA_HUMAN	342-383	42	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:264
 aligned with MICA_HUMAN | Q29983 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:274
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293    
           MICA_HUMAN    24 EPHSLRYNLTVLSWDGSVQSGFLTEVHLDGQPFLRCDRQKCRAKPQGQWAEDVLGNKTWDRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLSQNLETKEWTMPQSSRAQTLAMNVRNFLKEDAMKTKTHYHAMHADCLQELRRYLKSGVVLRRTVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGNGTYQTWVATRICQGEEQRFTCYMEHSGNHSTHPVPS 297
               SCOP domains d1b3ja2 A:1-180 Class I MHC homolog                                                                                                                                                 d1b3ja1 A:181-274 Class I MHC homolog, alpha-3 domain                                          SCOP domains
               CATH domains 1b3jA01 A:1-180 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                         1b3jA02 A:181-274 Immunoglobulins                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.......eeeeeee..eeeeee....eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee.....eeeeeeeee..eeeeeee....eee.......hhhhhhhhhhhhhhh.----------.hhhhhhhhhhh...........eeeeee........eeeeeeeee....eeeeeee.........eee......hhh.eeeeeeee.....hhheeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -----P-------G---------A-G---------Y------------------------------------------------------R-------------K--------R-------V-SE---V------------I--------V---------------------E-SI----R------------------------S-C-R--I-T-----L--------S--------------------R----S-----------G--A--- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1------------------------------------------------------------------------------------Exon 1.5b  PDB: A:86-182 (gaps) UniProt: 109-205                                                 -------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: A:1-86 UniProt: 24-109                                                 -----------------------------------------------------------------------------------------------Exon 1.6  PDB: A:182-274 UniProt: 205-298 [INCOMPLETE]                                        Transcript 1 (2)
                 1b3j A   1 EPHSLRYNLTVLSWDGSVQSGFLTEVHLDGQPFLRCDRQKCRAKPQGQWAEDVLGNKTWDRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLSQNLETKEWTMPQSSRAQTLAMNVRNFLKEDAM----------ADCLQELRRYLKSGVVLRRTVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGNGTYQTWVATRICQGEEQRFTCYMEHSGNHSTHPVPS 274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150|        - |     170       180       190       200       210       220       230       240       250       260       270    
                                                                                                                                                                                151        162

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 (402)

Homologous Superfamily: Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1 (400)

Human (Homo sapiens) (249)

1b3jA01

A:1-180

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1b3jA02

A:181-274

(no "Pfam Domain" information available for 1B3J)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MICA_HUMAN | Q29983)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0030881	beta-2-microglobulin binding	Interacting selectively and non-covalently with beta-2-microglobulin.
	GO:0046703	natural killer cell lectin-like receptor binding	Interacting selectively and non-covalently with a lectin-like natural killer cell receptor.
	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:0001913	T cell mediated cytotoxicity	The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	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:0006974	cellular response to DNA damage stimulus	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 damage to its DNA from environmental insults or errors during metabolism.
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0046629	gamma-delta T cell activation	The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	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:0002418	immune response to tumor cell	An immune system process that functions in the response of an organism to a tumor cell.
	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:0042267	natural killer cell mediated cytotoxicity	The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
	GO:0032815	negative regulation of natural killer cell activation	Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation.
	GO:0045953	negative regulation of natural killer cell mediated cytotoxicity	Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity.
	GO:0050776	regulation of immune response	Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0009408	response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	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.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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:0005887	integral component of plasma membrane	The component of the plasma 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.

Asymmetric/Biological Unit
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Description

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