2CDF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE-SPECIFIC T CELL RECEPTORS (TCR 5E)

Authors :   S. D. Gadola, M. Koch, J. Marles-Wright, N. M. Lissin, D. Sheperd, G. Mat K. Harlos, P. M. Villiger, D. I. Stuart, B. K. Jakobsen, V. Cerundolo, E

Date :   23 Jan 06 (Deposition) - 07 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Cell Receptor, Cd1D, Alpha-Galactosylceramide, Non-Canonical Tcr, Tcr, T Cell Receptor, Mhc Class I, Natural Killer T Cell, Tcr 5E (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Gadola, M. Koch, J. Marles-Wright, N. M. Lissin, D. Sheperd, G. Matulis, K. Harlos, P. M. Villiger, D. I. Stuart, B. K. Jakobsen, V. Cerundolo, E. Y. Jones
Structrue And Binding Kinetics Of Three Different Human Cd1D-Alpha-Galactosylceramide-Specific T Cell Receptors
J. Exp. Med. V. 203 699 2006
PubMed-ID: 16520393 | Reference-DOI: 10.1084/JEM.20052369

Molecule 1 - TCR 5E
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11

Molecule 2 - TCR 5E
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2CDF)

(no "Site" information available for 2CDF)

Asymmetric/Biological Unit

No.	Residues
1	A:24	-	A:90
2	A:137	-	A:187
3	A:162	-	B:172
4	B:24	-	B:92
5	B:146	-	B:211

Asymmetric/Biological Unit

No.	Residues
1	Ser A:8	-	Pro A:9
2	Lys A:182	-	Ser A:183
3	Thr B:8	-	Pro B:9
4	Tyr B:152	-	Pro B:153

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

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

(no "Exon" information available for 2CDF)

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:191
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:191
                                                                                                                                           1                                                                               
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79 
            TCA_HUMAN     - ---------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNN  80
               SCOP domains d2cdfa1 A:3-115 automated matches                                                                                d2cdfa2 A:116-193 automated matches                                            SCOP domains
               CATH domains 2cdfA01 A:3-114 Immunoglobulins                                                                                 ------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeee.....eeee..eeeee.....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeeee.......eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdf A   3 NQVEQSPQFLSIQEGENLTVYCNSSSVFSSLQWYRQEPGEGPVLLVTVVTGGEVKKLKRLTFQFGDARKDSSLHITAAQPGDTGLYLCAGADRGSTLGRLYFGRGTQLTVWPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNN 193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:244
                                                                                                                                              1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126    
          TRBC1_HUMAN     - ------------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains d2cdfb1 B:2-116 automated matches                                                                                  d2cdfb2 B:117-245 automated matches                                                                                               SCOP domains
               CATH domains 2cdfB01 B:2-116 Immunoglobulins                                                                                    2cdfB02 B:117-242 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.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cdf B   2 EADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDLSSESTVSRIRTEHFPLTLESARPSHTSQYLCASSEFRDGNEKLFFGSGTQLSVLEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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(

)

Folds(

)

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	d2cdfa1	A:3-115
1b	d2cdfa2	A:116-193
1c	d2cdfb1	B:2-116
1d	d2cdfb2	B:117-245

Asymmetric/Biological 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	2cdfA01	A:3-114
1b	2cdfB01	B:2-116
1c	2cdfB02	B:117-242

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

Asymmetric/Biological 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 (TRBC1_HUMAN | P01850)

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:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2cdf)

	Sites
(no "Sites" information available for 2cdf)

	Cis Peptide Bonds
		Lys A:182 - Ser A:183	[ RasMol ]
		Ser A:8 - Pro A:9	[ RasMol ]
		Thr B:8 - Pro B:9	[ RasMol ]
		Tyr B:152 - Pro B:153	[ RasMol ]

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	2cdf
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	TCA_HUMAN \| P01848
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	TRBC1_HUMAN \| P01850
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1ao7	COMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND HLA-A 0201
1b88	V-ALPHA 2.6 MOUSE T CELL RECEPTOR (TCR ) DOMAIN
1bd2	COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND MHC CLASS I MOLECULE HLA-A 0201
1bwm	A SINGLE-CHAIN T CELL RECEPTOR
1cd1	CD1(MOUSE) ANTIGEN PRESENTING MOLECULE
1d9k	CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I- AK/CA
1fo0	MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX
1fyt	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR1
1g6r	A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN ASUPERAGONIST TCR/MHC COMPLEX
1h5b	T CELL RECEPTOR VALPHA11 (AV11S5) DOMAIN
1hxm	CRYSTAL STRUCTURE OF A HUMAN VGAMMA9/VDELTA2 T CELL RECEPTOR
1j8h	CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELLRECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS IIMOLECULE, HLA-DR4
1kb5	MURINE T-CELL RECEPTOR VARIABLE DOMAIN/FAB COMPLEX
1kgc	IMMUNE RECEPTOR
1kj2	MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX
1ktk	COMPLEX OF STREPTOCOCCAL PYROGENIC ENTEROTOXIN C (SPEC)WITH A HUMAN T CELL RECEPTOR BETA CHAIN (VBETA2.1)
1l0y	T CELL RECEPTOR BETA CHAIN COMPLEXED WITH SUPERANTIGEN SPEASOAKED WITH ZINC
1lp9	XENOREACTIVE COMPLEX AHIII 12.2 TCR BOUND TO P1049/HLA-A2.1
1mi5	THE CRYSTAL STRUCTURE OF LC13 TCR IN COMPLEX WITH HLAB8-EBVPEPTIDE COMPLEX
1mwa	2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX
1nam	MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULECOMPLEX
1nfd	AN ALPHA-BETA T CELL RECEPTOR (TCR) HETERODIMER IN COMPLEX WITH AN ANTI-TCR FAB FRAGMENT DERIVED FROM A MITOGENIC ANTIBODY
1qrn	CRYSTAL STRUCTURE OF HUMAN A6 TCR COMPLEXED WITH HLA-A2 BOUND TO ALTERED HTLV-1 TAX PEPTIDE P6A
1qse	STRUCTURE OF HUMAN A6-TCR BOUND TO HLA- A2 COMPLEXED WITH ALTERED HTLV-1 TAX PEPTIDE V7R
1qsf	STRUCTURE OF A6-TCR BOUND TO HLA-A2 COMPLEXED WITH ALTERED HTLV-1 TAX PEPTIDE Y8A
1tcr	MURINE T-CELL ANTIGEN RECEPTOR 2C CLONE
1tvd	VARIABLE DOMAIN OF T CELL RECEPTOR DELTA CHAIN
1ymm	TCR/HLA-DR2B/MBP-PEPTIDE COMPLEX
1ypz	IMMUNE RECEPTOR
1z5l	STRUCTURE OF A HIGHLY POTENT SHORT-CHAIN GALACTOSYLCERAMIDE AGONIST BOUND TO CD1D
1zhn	CRYSTAL STRUCTURE OF MOUSE CD1D BOUND TO THE SELF LIGANDPHOSPHATIDYLCHOLINE
1zt4	THE CRYSTAL STRUCTURE OF HUMAN CD1D WITH AND WITHOUT ALPHA-GALACTOSYLCERAMIDE
2akr	STRUCTURAL BASIS OF SULFATIDE PRESENTATION BY MOUSE CD1D
2axh	CRYSTAL STRUCTURES OF T CELL RECEPTOR BETA CHAINS RELATEDTO RHEUMATOID ARTHRITIS
2axj	CRYSTAL STRUCTURES OF T CELL RECEPTOR BETA CHAINS RELATEDTO RHEUMATOID ARTHRITIS
2bnq	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2bnr	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2bnu	STRUCTURAL AND KINETIC BASIS FOR HIGHTENED IMMUNOGENICITY OF T CELL VACCINES
2cde	STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE SPECIFIC T CELL RECEPTORS - INKT-TCR
2cdg	STRUCTURE AND BINDING KINETICS OF THREE DIFFERENT HUMAN CD1D-ALPHA-GALACTOSYLCERAMIDE- SPECIFIC T CELL RECEPTORS (TCR 5B)
2ckb	STRUCTURE OF THE 2C/KB/DEV8 COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (7, 13)

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