2ATP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CD8AB HETERODIMER

Authors :   H. C. Chang, K. Tan, J. Ouyang, E. Parisini, J. H. Liu, Y. Le, X. Wang, E. L. J. H. Wang

Date :   25 Aug 05 (Deposition) - 27 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E  (1x)
Biol. Unit 2: C,D,F  (1x)

Keywords :   Cd8Ab, Cd8Aa, Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. C. Chang, K. Tan, J. Ouyang, E. Parisini, J. H. Liu, Y. Le, X. Wang, E. L. Reinherz, J. H. Wang
Structural And Mutational Analyses Of A Cd8Alphabeta Heterodimer And Comparison With The Cd8Alphaalpha Homodimer
Immunity V. 23 661 2005
PubMed-ID: 16356863 | Reference-DOI: 10.1016/J.IMMUNI.2005.11.002

Molecule 1 - T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14
	Expression System Strain	:	CHO-LEC 3.8.2.1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	CD8A ECTODOMAIN FRAGMENT
	Gene	:	CD8A, LYT-2, LYT2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	T-CELL SURFACE GLYCOPROTEIN LYT-2

Molecule 2 - ARTIFACT LINKER
	Chains	:	E, F
	Engineered	:	YES
	Fragment	:	A PEPTIDE USED TO CONNECT CD8A C-TERMINAL AND CD8B N- TERMINAL
	Other Details	:	SYNTHETIC LINKER
	Synthetic	:	YES

Molecule 3 - T-CELL SURFACE GLYCOPROTEIN CD8 BETA CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Plasmid	:	PEE14
	Expression System Strain	:	CHO-LEC 3.8.2.1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	PLASMID
	Fragment	:	CD8B ECTODOMAIN FRAGMENT
	Gene	:	CD8B, LYT-3, LYT3
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	T-CELL SURFACE GLYCOPROTEIN LYT-3, T-CELL MEMBRANE GLYCOPROTEIN LY-3

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B			E
Biological Unit 2 (1x)	:			C	D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 2)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:40 , ASN A:42 , SER A:44 , GLU A:95 , ARG E:23	BINDING SITE FOR RESIDUE NAG A 242
2	AC2	SOFTWARE	ASN C:42 , SER C:44 , GLU C:95	BINDING SITE FOR RESIDUE NAG C 242
3	AC3	SOFTWARE	ASN D:13	BINDING SITE FOR RESIDUE NAG D 213

Asymmetric Unit

No.	Residues
1	A:26	-	A:102
2	B:20	-	B:96
3	C:26	-	C:102
4	D:20	-	D:96

Asymmetric Unit

No.	Residues
1	Phe A:10	-	Pro A:11
2	Thr B:4	-	Pro B:5
3	Ser B:101	-	Pro B:102
4	Phe C:10	-	Pro C:11
5	Thr D:4	-	Pro D:5
6	Ser D:101	-	Pro D:102

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CD8B_MOUSE_001 *	R	98	S	CD8B_MOUSE	---	---	B/D	R	77	S
2	UniProt	VAR_CD8A_MOUSE_001 *	M	105	V	CD8A_MOUSE	---	---	A/C	M	78	V
	* ID not provided by source

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CD8B_MOUSE_001 *	R	98	S	CD8B_MOUSE	---	---	B	R	77	S
2	UniProt	VAR_CD8A_MOUSE_001 *	M	105	V	CD8A_MOUSE	---	---	A	M	78	V
	* ID not provided by source

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CD8B_MOUSE_001 *	R	98	S	CD8B_MOUSE	---	---	D	R	77	S
2	UniProt	VAR_CD8A_MOUSE_001 *	M	105	V	CD8A_MOUSE	---	---	C	M	78	V
	* ID not provided by source

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

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

(no "Exon" information available for 2ATP)

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
	(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:118
 aligned with CD8A_MOUSE | P01731 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:118
                                    40        50        60        70        80        90       100       110       120       130       140        
           CD8A_MOUSE    31 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQK 148
               SCOP domains d2atpa_ A: CD8                                                                                                         SCOP domains
               CATH domains 2atpA00 A:4-121 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeeee......eeeeeeee........eeeeeee.....eee..........eeeee...eeeeee........eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2atp A   4 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQK 121
                                    13        23        33        43        53        63        73        83        93       103       113

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with CD8B_MOUSE | P10300 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:115
                                    31        41        51        61        71        81        91       101       111       121       131     
           CD8B_MOUSE    22 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVV 136
               SCOP domains d2atpb1 B:1-115 CD8                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeee..eeee.....eeeeeee.......eeeeeeeee....eeeeeeeeee...eeee.hhhh....eeee.......eeee...hhhhheeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S-------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2atp B   1 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVV 115
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with CD8A_MOUSE | P01731 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:119
                                    40        50        60        70        80        90       100       110       120       130       140         
           CD8A_MOUSE    31 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQKV 149
               SCOP domains d2atpc_ C: CD8                                                                                                          SCOP domains
               CATH domains 2atpC00 C:4-122 Immunoglobulins                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........eeeeeeee......eeeeeee........eeeeee......eee.hhhh....eeeeee...eeeeee...hhhh.eeeeeeeee..eeee...eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V-------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2atp C   4 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQKV 122
                                    13        23        33        43        53        63        73        83        93       103       113

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with CD8B_MOUSE | P10300 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:115
                                    31        41        51        61        71        81        91       101       111       121       131     
           CD8B_MOUSE    22 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVV 136
               SCOP domains d2atpd_ D: CD8                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeee....eeeeee.....---.eeeeeeeee..eeeeeeeeeee...eeee.....hhh.eeee.......eeee...hhhhheeeeeeee....eee...eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S-------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2atp D   1 LIQTPSSLLVQTNHTAKMSCEVKSIS---SIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVV 115
                                    10        20     |  30        40        50        60        70        80        90       100       110     
                                                    26  30

Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2atp E  23 RKDGSSA  29

Chain F from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 2atp F  28 SA  29

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

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

Protein domain: CD8 (10)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d2atpa_	A:
1b	d2atpc_	C:

Mouse (Mus musculus), beta-chain [TaxId: 10090] (2)

2a	d2atpb1	B:1-115
2b	d2atpd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	2atpA00	A:4-121
1b	2atpC00	C:4-122

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (CD8A_MOUSE | P01731)

molecular function
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
	GO:0042110	T cell activation	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0002456	T cell mediated immunity	Any process involved in the carrying out of an immune response by a T cell.
	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:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0045065	cytotoxic T cell differentiation	The process in which a relatively unspecialized T cell acquires specialized features of a cytotoxic T cell.
	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: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:0050850	positive regulation of calcium-mediated signaling	Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (CD8B_MOUSE | P10300)

molecular function
	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: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: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.
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: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 D:101 - Pro D:102	[ RasMol ]
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		Thr D:4 - Pro D:5	[ RasMol ]

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UniProtKB/Swiss-Prot
	CD8A_MOUSE \| P01731	:	1bqh 1nez 2arj 3b9k 3dmm
	CD8B_MOUSE \| P10300	:	3b9k 3dmm

1bqh	MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8
1nez	THE CRYSTAL STRUCTURE OF A TL/CD8AA COMPLEX AT 2.1A RESOLUTION:IMPLICATIONS FOR MEMORY T CELL GENERATION, CO- RECEPTOR PREFERENCE AND AFFINITY

Description

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Ligands, Modified Residues, Ions (1, 3)

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SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

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