2PYF - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF HIGH AFFINITY HUMAN T-CELL RECEPTORS BOUND TO PMHC REVEALNATIVE DIAGONAL BINDING GEOMETRY UNBOUND TCR CLONE 5-1

Authors :   M. Sami, P. J. Rizkallah, S. Dunn, Y. Li, R. Moysey, A. Vuidepot, E. Basto P. Todorov, P. Molloy, F. Gao, J. M. Boulter, B. K. Jakobsen

Date :   16 May 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   T-Cell Receptor, Cdr3, Phage Display, Mutant, High Affinity, Ny-Eso- 1, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sami, P. J. Rizkallah, S. Dunn, P. Molloy, R. Moysey, A. Vuidepot, E. Baston, P. Todorov, L. Yi, F. Gao, J. M. Boulter, B. K. Jakobsen
Crystal Structures Of High Affinity Human T-Cell Receptors Bound To Peptide Major Histocompatibility Complex Reveal Native Diagonal Binding Geometry
Protein Eng. Des. Sel. V. 20 397 2007
PubMed-ID: 17644531 | Reference-DOI: 10.1093/PROTEIN/GZM033

Molecule 1 - T-CELL RECEPTOR, ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGMT7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - T-CELL RECEPTOR, BETA CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGMT7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
2	PGE	4	Ligand/Ion	TRIETHYLENE GLYCOL
3	SO4	6	Ligand/Ion	SULFATE ION

(no "Site" information available for 2PYF)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:90
2	A:137	-	A:187
3	A:162	-	B:168
4	B:21	-	B:89
5	B:142	-	B:207

Asymmetric/Biological Unit

No.	Residues
1	Ile A:7	-	Pro A:8
2	Thr B:5	-	Pro B:6
3	Tyr B:148	-	Pro B:149

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

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

(no "Exon" information available for 2PYF)

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:205
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:206
                                                                                                                                             1                                                                                            
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87      
            TCA_HUMAN     - -----------------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPE  93
               SCOP domains d2pyfa1 A:1-115 automated matches                                                                                  d2pyfa2 A:116-205 automated matches                                                         SCOP domains
               CATH domains 2pyfA01 A:1-114 Immunoglobulins                                                                                   -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------DUF1968-2pyfA01 A:121-197                                                    --------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....eeeeeeeee.....eeeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee........ee...eeeeee........eeeeeee......eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhhh.....-........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyf A   1 KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGSSTLYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIP-DTFFPSPE 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      |199      
                                                                                                                                                                                                                              197 |       
                                                                                                                                                                                                                                198

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:241
                                                                                                                                           1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99       109       119       129 
          TRBC1_HUMAN     - ---------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains d2pyfb1 B:1-113 automated matches                                                                                d2pyfb2 B:114-241 automated matches                                                                                              SCOP domains
               CATH domains 2pyfB01 B:1-112 Immunoglobulins                                                                                 2pyfB02 B:113-238 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeeeee..eeee.......ee.........eee...hhhhheeeeeeee........ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyf B   1 GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGTTDQGEVPNGYNVSRSTIEDFPLRLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

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)

d2pyfa1

A:1-115

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

Protein domain: automated matches (652)

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

2a	d2pyfa2	A:116-205
2b	d2pyfb2	B:114-241

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Human (Homo sapiens) [TaxId: 9606] (85)

d2pyfb1

B:1-113

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	2pyfA01	A:1-114
1b	2pyfB01	B:1-112
1c	2pyfB02	B:113-238

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF1968] (16)

Family: DUF1968 (16)

Homo sapiens (Human) (14)

DUF1968-2pyfA01

A:121-197

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

	Cis Peptide Bonds
		Ile A:7 - Pro A:8	[ RasMol ]
		Thr B:5 - Pro B:6	[ RasMol ]
		Tyr B:148 - Pro B:149	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (3, 3)

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SCOP Domains (3, 4)

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