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Asym./Biol. Unit (Jmol Viewer)

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Title :   NKG2D IN COMPLEX WITH ULBP3

Authors :   S. Radaev, P. Sun

Date :   08 Nov 01 (Deposition) - 09 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Protein-Protein Complex, C-Type Lectin-Like Receptor, Mhc Class I-Like Molecule, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Radaev, B. Rostro, A. G. Brooks, M. Colonna, P. D. Sun
Conformational Plasticity Revealed By The Cocrystal Structure Of Nkg2D And Its Class I Mhc-Like Ligand Ulbp3.
Immunity V. 15 1039 2001
PubMed-ID: 11754823 | Reference-DOI: 10.1016/S1074-7613(01)00241-2
(for further references see the PDB file header)

Molecule 1 - NKG2-D TYPE II INTEGRAL MEMBRANE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACTIVATING NK RECEPTOR NKG2D

Molecule 2 - ULBP3 PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CLASS I MHC-LIKE MOLECULE ULBP3

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GSH	1	Ligand/Ion	GLUTATHIONE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS C:11 , CYS C:109 , GLU C:110 , ASP C:112 , LEU C:174 , LEU C:178 , MET C:179	BINDING SITE FOR RESIDUE GSH C 999

Asymmetric/Biological Unit

No.	Residues
1	A:96	-	A:105
2	A:99	-	A:110
3	A:127	-	A:211
4	A:189	-	A:203
5	B:96	-	B:105
6	B:99	-	B:110
7	B:127	-	B:211
8	B:189	-	B:203
9	C:30	-	C:46
10	C:107	-	C:170

(no "Cis Peptide Bond" information available for 1KCG)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030738	N	177	S	NKG2D_HUMAN	Polymorphism	2306182	A/B	N	177	S

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	NKG2D_HUMAN	106-212	2	A:106-212 B:106-212

Asymmetric/Biological Unit (7, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000240618	1	ENSE00001524992	chr12:10542640-10542542	99	NKG2D_HUMAN	-	0	0	-	-
1.2	ENST00000240618	2	ENSE00002198225	chr12:10541474-10541370	105	NKG2D_HUMAN	1-14	14	0	-	-
1.3	ENST00000240618	3	ENSE00001656271	chr12:10539609-10539502	108	NKG2D_HUMAN	14-50	37	0	-	-
1.4	ENST00000240618	4	ENSE00001160615	chr12:10532391-10532299	93	NKG2D_HUMAN	50-81	32	0	-	-
1.5	ENST00000240618	5	ENSE00001160608	chr12:10532081-10532046	36	NKG2D_HUMAN	81-93	13	1	- B:93-93	- 1
1.6a	ENST00000240618	6a	ENSE00001160601	chr12:10531304-10531153	152	NKG2D_HUMAN	93-143	51	2	A:94-143 B:93-143	50 51
1.7	ENST00000240618	7	ENSE00000821886	chr12:10530834-10530731	104	NKG2D_HUMAN	144-178	35	2	A:144-178 B:144-178	35 35
1.8	ENST00000240618	8	ENSE00001160593	chr12:10525830-10524953	878	NKG2D_HUMAN	178-216	39	2	A:178-215 B:178-215	38 38

2.3c	ENST00000367339	3c	ENSE00001444257	chr6:150390231-150390115	117	N2DL3_HUMAN	1-30	30	1	C:9-9	1
2.4a	ENST00000367339	4a	ENSE00000896365	chr6:150387298-150387035	264	N2DL3_HUMAN	30-118	89	1	C:9-89	81
2.5b	ENST00000367339	5b	ENSE00000896364	chr6:150386809-150386534	276	N2DL3_HUMAN	118-210	93	1	C:98-186	89
2.6a	ENST00000367339	6a	ENSE00000896363	chr6:150385849-150385743	107	N2DL3_HUMAN	210-244	35	0	-	-
2.7a	ENST00000367339	7a	ENSE00001444256	chr6:150384487-150384286	202	N2DL3_HUMAN	-	0	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with NKG2D_HUMAN | P26718 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:122
                                   103       113       123       133       143       153       163       173       183       193       203       213  
          NKG2D_HUMAN    94 SYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
               SCOP domains d1kcga_ A: NK cell-activating receptor nkg2d                                                                               SCOP domains
               CATH domains 1kcgA00 A:94-215 Mannose-Binding Protein A, subunit A                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eee..eeeeeeeeeehhhhhhhhhhh.............hhhhhh...eee..eee......eee...........eee......eeeee...eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------S-------------------------------------- SAPs(SNPs)
                    PROSITE ------------C_TYPE_LECTIN_2  PDB: A:106-212 UniProt: 106-212                                                           --- PROSITE
           Transcript 1 (1) --------------------------------------------------Exon 1.7  PDB: A:144-178           ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.6a  PDB: A:94-143 UniProt: 93-143          ----------------------------------Exon 1.8  PDB: A:178-215 [INCOMPLETE]  Transcript 1 (2)
                 1kcg A  94 SYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   103       113       123       133       143       153       163       173       183       193       203       213

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with NKG2D_HUMAN | P26718 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:123
                                   102       112       122       132       142       152       162       172       182       192       202       212   
          NKG2D_HUMAN    93 ESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
               SCOP domains d1kcgb_ B: NK cell-activating receptor nkg2d                                                                                SCOP domains
               CATH domains 1kcgB00 B:93-215 Mannose-Binding Protein A, subunit A                                                                       CATH domains
           Pfam domains (1) -----------------------Lectin_C-1kcgB01 B:116-213                                                                        -- Pfam domains (1)
           Pfam domains (2) -----------------------Lectin_C-1kcgB02 B:116-213                                                                        -- Pfam domains (2)
         Sec.struct. author .eee.......ee...eeeeeeeeeehhhhhhhhhhh...ee........hhhhhhh..eeeeeeee......eee...........eeee.....eeeee...eeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------S-------------------------------------- SAPs(SNPs)
                    PROSITE -------------C_TYPE_LECTIN_2  PDB: B:106-212 UniProt: 106-212                                                           --- PROSITE
           Transcript 1 (1) 1--------------------------------------------------Exon 1.7  PDB: B:144-178           ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.6a  PDB: B:93-143 UniProt: 93-143           ----------------------------------Exon 1.8  PDB: B:178-215 [INCOMPLETE]  Transcript 1 (2)
                 1kcg B  93 ESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSKEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYICMQRT 215
                                   102       112       122       132       142       152       162       172       182       192       202       212

Chain C from PDB  Type:PROTEIN  Length:170
 aligned with N2DL3_HUMAN | Q9BZM4 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:178
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
          N2DL3_HUMAN    30 DAHSLWYNFTIIHLPRHGQQWCEVQSQVDQKNFLSYDCGSDKVLSMGHLEEQLYATDAWGKQLEMLREVGQRLRLELADTELEDFTPSGPLTLQVRMSCECEADGYIRGSWQFSFDGRKFLLFDSNNRKWTVVHAGARRMKEKWEKDSGLTTFFKMVSMRDCKSWLRDFLMHRKKRLE 207
               SCOP domains d1kcgc_ C: Class I MHC-related molecule Ulbp3                                                                                                                                      SCOP domains
               CATH domains 1kcgC00 C:9-186 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A        , domain 1                                                                                CATH domains
               Pfam domains MHC_I-1kcgC01 C:9-185                                                                                                                                                            - Pfam domains
         Sec.struct. author ..eeeeeeeeee.........eeeeeee..eeeeeee....ee............hhhhhhhhhhhhhhhhhhhhhhhh..--------..eeeeeeeeee......eeeeeee....eeeeee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) 2---------------------------------------------------------------------------------------Exon 2.5b  PDB: C:98-186 UniProt: 118-210 [INCOMPLETE]                                     Transcript 2 (1)
           Transcript 2 (2) Exon 2.4a  PDB: C:9-89 UniProt: 30-118 [INCOMPLETE]                                      ----------------------------------------------------------------------------------------- Transcript 2 (2)
                 1kcg C   9 DAHSLWYNFTIIHLPRHGQQWCEVQSQVDQKNFLSYDCGSDKVLSMGHLEEQLYATDAWGKQLEMLREVGQRLRLELADTE--------PLTLQVRMSCECEADGYIRGSWQFSFDGRKFLLFDSNNRKWTVVHAGARRMKEKWEKDSGLTTFFKMVSMRDCKSWLRDFLMHRKKRLE 186
                                    18        28        38        48        58        68        78        88|       98       108       118       128       138       148       158       168       178        
                                                                                                           89       98

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: C_Lectin (98)

Family: Lectin_C (85)

Homo sapiens (Human) (39)

1a	Lectin_C-1kcgB01	B:116-213
1b	Lectin_C-1kcgB02	B:116-213

Clan: MHC (252)

Family: MHC_I (210)

Homo sapiens (Human) (144)

MHC_I-1kcgC01

C:9-185

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NKG2D_HUMAN | P26718)

molecular function
	GO:0042288	MHC class I protein binding	Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0032394	MHC class Ib receptor activity	Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families.
	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:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
	GO:0031295	T cell costimulation	The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
	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:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	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: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: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:0030101	natural killer cell activation	The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
	GO:0034260	negative regulation of GTPase activity	Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
	GO:2000502	negative regulation of natural killer cell chemotaxis	Any process that stops, prevents or reduces the frequency, rate or extent of natural killer cell chemotaxis.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0032729	positive regulation of interferon-gamma production	Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0030887	positive regulation of myeloid dendritic cell activation	Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation.
	GO:0045954	positive regulation of natural killer cell mediated cytotoxicity	Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
	GO:0002860	positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated cytotoxicity directed against tumor cell target.
	GO:0045429	positive regulation of nitric oxide biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide.
	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: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.
	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.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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: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.

Chain C (N2DL3_HUMAN | Q9BZM4)

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:0046703	natural killer cell lectin-like receptor binding	Interacting selectively and non-covalently with a lectin-like natural killer cell receptor.
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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0030101	natural killer cell activation	The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor.
	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: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: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:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0046658	anchored component of plasma membrane	The component of the plasma membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group, that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	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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	NKG2D_HUMAN \| P26718
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	NKG2D_HUMAN \| P26718	:	1hyr 1mpu 4pdc 4s0u

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

Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (10, 10)

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