2EYS - JenaLib

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Title :   A STRUCTURAL BASIS FOR SELECTION AND CROSS-SPECIES REACTIVITY OF THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION

Authors :   L. Kjer-Nielsen, N. A. Borg

Date :   09 Nov 05 (Deposition) - 21 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

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

Keywords :   Natural Killer T Cell Receptor, Nkt Cell Receptor, Nkt15, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Kjer-Nielsen, N. A. Borg, D. G. Pellicci, T. Beddoe, L. Kostenko, C. S. Clements, N. A. Williamson, M. J. Smyth, G. S. Besra, H. H. Reid, M. Bharadwaj, D. I. Godfrey, J. Rossjohn, J. Mccluskey
A Structural Basis For Selection And Cross-Species Reactivity Of The Semi-Invariant Nkt Cell Receptor In Cd1D/Glycolipid Recognition
J. Exp. Med. V. 203 661 2006
PubMed-ID: 16505140 | Reference-DOI: 10.1084/JEM.20051777
(for further references see the PDB file header)

Molecule 1 - NKT15
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - NKT15
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:169 , HIS B:170 , SER B:171	BINDING SITE FOR RESIDUE ACY B 1001
2	AC2	SOFTWARE	ARG A:60 , GLY B:166 , ARG B:212 , HOH B:1018 , HOH B:1022	BINDING SITE FOR RESIDUE ACY B 1002

Asymmetric Unit

No.	Residues
1	A:22	-	A:90
2	A:139	-	A:189
3	A:164	-	B:174
4	B:23	-	B:92
5	B:148	-	B:213

Asymmetric Unit

No.	Residues
1	Ser A:6	-	Pro A:7
2	Ser A:27	-	Pro A:28
3	Thr B:7	-	Pro B:8
4	Tyr B:154	-	Pro B:155

(no "SAP(SNP)/Variant" information available for 2EYS)

(no "PROSITE Motif" information available for 2EYS)

(no "Exon" information available for 2EYS)

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
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Chain A from PDB  Type:PROTEIN  Length:202
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:202
                                                                                                                                            1                                                                                         
                                     -         -         -         -         -         -         -         -         -         -         -  |      8        18        28        38        48        58        68        78        88  
            TCA_HUMAN     - ----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP  90
               SCOP domains d2eysa1 A:1-117 automated matches                                                                                 d2eysa2 A:118-205 automated matches                                                      SCOP domains
               CATH domains 2eysA01 A:1-116 Immunoglobulins                                                                                  ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeee........eeeeee...............eee...eeeee....eeeeeeeeee.....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eys A   1 NQVEQSPQSLIILEGKNCTLQCNYTVSPFSNLRWYKQDTGRGPVSLTIMTFSENTKSNGRYTATLDADTKQSSLHITASQLSDSASYICVVSDRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 205
                                    10        20        30        40        50        60|       71        81        91       103       113       123       133       143       153       163       173       183       193       203  
                                                                                      60|                                   100|                                                                                                      
                                                                                       62                                    103

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TRBC2_HUMAN | A0A5B9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:243
                                                                                                                                              1                                                                                                                                
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126   
          TRBC2_HUMAN     - ------------------------------------------------------------------------------------------------------------------DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 129
               SCOP domains d2eysb1 B:3-119 automated matches                                                                                  d2eysb2 B:120-247 automated matches                                                                                              SCOP domains
               CATH domains 2eysB01 B:3-118 Immunoglobulins                                                                                   2eysB02 B:119-244 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee.......ee.........eee...hhhhheeeeeeeeee.....eeeee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eys B   3 DIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSGLRDRGLYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 247
                                    12        22        32        42        52        62||      73        83        93       103|      114       124       134       144       154       164       174       184       194       204       214       224       234       244   
                                                                                       63|                                   103|                                                                                                                                              
                                                                                        65                                    105

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	-	→ 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

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d2eysa1	A:1-117
1b	d2eysb1	B:3-119

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

2a	d2eysa2	A:118-205
2b	d2eysb2	B:120-247

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	2eysA01	A:1-116
1b	2eysB01	B:3-118
1c	2eysB02	B:119-244

(no "Pfam Domain" information available for 2EYS)

Asymmetric Unit(hide GO term definitions)

Chain A (TCA_HUMAN | P01848)

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:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	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.
cellular component
	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 B (TRBC2_HUMAN | A0A5B9)

cellular component
	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.

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		Ser A:6 - Pro A:7	[ RasMol ]
		Thr B:7 - Pro B:8	[ RasMol ]
		Tyr B:154 - Pro B:155	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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2eyr	THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION
2eyt	THE SEMI-INVARIANT NKT CELL RECEPTOR IN CD1D/GLYCOLIPID RECOGNITION

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