3B9K - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CD8ALPHA-BETA IN COMPLEX WITH YTS 156.7 FAB

Authors :   D. Shore, I. A. Wilson

Date :   05 Nov 07 (Deposition) - 11 Nov 08 (Release) - 22 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Immunoglobulin Domain, V-Set, Igsf Dimer, Glycoprotein, Immune Response, Membrane, Transmembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Shore, H. Issafras, E. Landais, L. Teyton, I. A. Wilson
The Crystal Structure Of Cd8 In Complex With Yts156. 7. 7 Fab And Interaction With Other Cd8 Antibodies Define The Bindin Mode Of Cd8 Alphabeta To Mhc Class I
J. Mol. Biol. V. 384 1190 2008
PubMed-ID: 18929574 | Reference-DOI: 10.1016/J.JMB.2008.09.069

Molecule 1 - FAB LIGHT CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	L, C
	Fragment	:	FAB FRAGMENT
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS RATTUS
	Organism Taxid	:	10117
	Strain	:	YTS156.7

Molecule 2 - FAB HEAVY CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	H, D
	Fragment	:	FAB FRAGMENT
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS RATTUS
	Organism Taxid	:	10117
	Strain	:	YTS156.7

Molecule 3 - T-CELL SURFACE GLYCOPROTEIN CD8 ALPHA CHAIN
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PRMHA3
	Expression System Strain	:	SC2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	IG-LIKE V-TYPE DOMAIN
	Gene	:	CD8A, LYT-2, LYT2
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	T-CELL SURFACE GLYCOPROTEIN LYT-2, CD8A ANTIGEN

Molecule 4 - T-CELL SURFACE GLYCOPROTEIN CD8 BETA CHAIN
	Chains	:	B, F
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Plasmid	:	PRMHA3
	Expression System Strain	:	SC2
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	IG-LIKE V-TYPE DOMAIN
	Gene	:	CD8B, CD8B1, LY-3, LYT-3, LYT3
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	T-CELL SURFACE GLYCOPROTEIN LYT-3, T-CELL MEMBRANE GLYCOPROTEIN LY-3, LYMPHOCYTE ANTIGEN 3, CD8B ANTIGEN

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	H	L
Biological Unit 1 (1x)	:	A	B					H	L
Biological Unit 2 (1x)	:			C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	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, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:42 , SER A:45 , GLU A:95	BINDING SITE FOR RESIDUE NAG A 242
2	AC2	SOFTWARE	ASN E:42 , SER E:44 , SER E:45 , LEU E:69	BINDING SITE FOR RESIDUE NAG E 242

Asymmetric Unit

No.	Residues
1	A:26	-	A:102
2	B:20	-	B:96
3	C:134	-	C:194
4	D:22	-	D:92
5	D:142	-	D:207
6	E:26	-	E:102
7	F:20	-	F:96
8	H:22	-	H:92
9	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:140	-	Pro L:141
3	Phe H:148	-	Pro H:149
4	Glu H:150	-	Pro H:151
5	Phe A:10	-	Pro A:11
6	Thr B:4	-	Pro B:5
7	Ser B:101	-	Pro B:102
8	Ser C:7	-	Pro C:8
9	Tyr C:140	-	Pro C:141
10	Phe D:148	-	Pro D:149
11	Glu D:150	-	Pro D:151
12	Phe E:10	-	Pro E:11
13	Thr F:4	-	Pro F:5
14	Ser F:101	-	Pro F: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/F	R	77	S
2	UniProt	VAR_CD8A_MOUSE_001 *	M	105	V	CD8A_MOUSE	---	---	A/E	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	---	---	F	R	77	S
2	UniProt	VAR_CD8A_MOUSE_001 *	M	105	V	CD8A_MOUSE	---	---	E	M	78	V
	* ID not provided by source

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACA_RAT	84-90	2	C:192-198 L:192-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACA_RAT	84-90	1	- L:192-198

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACA_RAT	84-90	1	C:192-198 -

(no "Exon" information available for 3B9K)

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 d3b9ka_ A: CD8                                                                                                         SCOP domains
               CATH domains 3b9kA00 A:4-121 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eee.....eeeeeeee......eeeeeee........eeeeee......eee.........eeeeee...eeeeee...hhhh.eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k A    4 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQK  121
                                    13        23        33        43        53        63        73        83        93       103       113

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with CD8B_MOUSE | P10300 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:117
                                    31        41        51        61        71        81        91       101       111       121       131       
          CD8B_MOUSE     22 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV  138
               SCOP domains d3b9kb_ B: CD8                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeee....eeeeee........eeeeeeee......eeeeeeeee....eee.........eeee.......eeee...hhhhheeeeeeee....eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k B    1 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV  117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with KACA_RAT | P01836 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                       1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103   
            KACA_RAT      - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSMEQLTSGGATVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLSLTKVEYERHNLYTCEVVHKTSSSPVVKSFNRNEC  106
               SCOP domains d3b9kc1 C:1-107 automated matches                                                                         d3b9kc2 C:108-214 automated matches                                                                         SCOP domains
               CATH domains 3b9kC01 C:1-108 Immunoglobulins                                                                            3b9kC02 C:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh....eeeeeee..eeeeeeee.hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k C    1 DIKMTQSPASLSASLGDKVTITCQASQNIDKYIAWYQQKPGKAPRQLIHYTSTLVSGTPSRFSGSGSGRDYTFSISSVESEDIASYYCLQYDTLYTFGAGTKLELKRADAAPTVSIFPPSMEQLTSGGATVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLSLTKVEYERHNLYTCEVVHKTSSSPVVKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90   ||  101       111       121       131       141       151       161       171       181       191       201       211   
                                                                                                                        94|                                                                                                                      
                                                                                                                         96

Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b9kD01 D:1-113 Immunoglobulins                                                                                      3b9kD02 D:114-230 Immunoglobulins                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeee........ee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeee.hhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k D    1 QVRLQESGPGLVQPSQTLSLTCSVSGFSLISDSVHWVRQPPGKGLEWMGGIWADGSTEYNSALKSRLSISRDTSKSQGFLKMNSLQTDDTAIYFCTSNRESYYFDYWGQGTMVTVSSAQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKAVEA  230
                                    10        20        30        40        50        60        70        80  |||   87        97   |   106       116       126   ||  138       148     ||161     ||174     ||188       198| ||   211       221 || 
                                                                                                            82A||               100A                           130|                  154|||    167|      180|          198| || 208|          223| 
                                                                                                             82B|                                               133                   156||     171       185           200 ||  210           229 
                                                                                                              82C                                                                      157|                               202|                    
                                                                                                                                                                                        160                                204

Chain E 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 d3b9ke_ E: CD8                                                                                                         SCOP domains
               CATH domains 3b9kE00 E:4-121 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eee.....eeeeeeee......eeeeeee........eeeeee......eeehhhhhh...eeeeee...eeeeee........eeeeeeeee..eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------V------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k E    4 APELRIFPKKMDAELGQKVDLVCEVLGSVSQGCSWLFQNSSSKLPQPTFVVYMASSHNKITWDEKLNSSKLFSAMRDTNNKYVLTLNKFSKENEGYYFCSVISNSVMYFSSVVPVLQK  121
                                    13        23        33        43        53        63        73        83        93       103       113

Chain F from PDB  Type:PROTEIN  Length:117
 aligned with CD8B_MOUSE | P10300 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:117
                                    31        41        51        61        71        81        91       101       111       121       131       
          CD8B_MOUSE     22 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV  138
               SCOP domains d3b9kf_ F: CD8                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eeeee....eeeeee........eeeeeeee......eeeeeeeee....eee.........eeee.......eeee...hhhhheeeeeeee....eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------S---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k F    1 LIQTPSSLLVQTNHTAKMSCEVKSISKLTSIYWLRERQDPKDKYFEFLASWSSSKGVLYGESVDKKRNIILESSDSRRPFLSIMNVKPEDSDFYFCATVGSPKMVFGTGTKLTVVDV  117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b9kH01 H:1-113 Immunoglobulins                                                                                      3b9kH02 H:114-230 Immunoglobulins                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeeee........ee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeee........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k H    1 QVRLQESGPGLVQPSQTLSLTCSVSGFSLISDSVHWVRQPPGKGLEWMGGIWADGSTEYNSALKSRLSISRDTSKSQGFLKMNSLQTDDTAIYFCTSNRESYYFDYWGQGTMVTVSSAQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKAVEA  230
                                    10        20        30        40        50        60        70        80  |||   87        97   |   106       116       126   ||  138       148     ||161     ||174     ||188       198| ||   211       221 || 
                                                                                                            82A||               100A                           130|                  154|||    167|      180|          198| || 208|          223| 
                                                                                                             82B|                                               133                   156||     171       185           200 ||  210           229 
                                                                                                              82C                                                                      157|                               202|                    
                                                                                                                                                                                        160                                204

Chain L from PDB  Type:PROTEIN  Length:213
 aligned with KACA_RAT | P01836 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                       1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103   
            KACA_RAT      - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSMEQLTSGGATVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLSLTKVEYERHNLYTCEVVHKTSSSPVVKSFNRNEC  106
               SCOP domains d3b9kl1 L:1-107 automated matches                                                                         d3b9kl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 3b9kL01 L:1-108 Immunoglobulins                                                                            3b9kL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee.....ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh....eeeeee.......eee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3b9k L    1 DIKMTQSPASLSASLGDKVTITCQASQNIDKYIAWYQQKPGKAPRQLIHYTSTLVSGTPSRFSGSGSGRDYTFSISSVESEDIASYYCLQYDTLYTFGAGTKLELKRADAAPTVSIFPPSMEQLTSGGATVVCFVNNFYPRDISVKWKIDGSEQRDGVLDSVTDQDSKDSTYSMSSTLSLTKVEYERHNLYTCEVVHKTSSSPVVKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90   ||  101       111       121       131       141       151       161       171       181       191       201       211   
                                                                                                                        94|                                                                                                                      
                                                                                                                         96

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: automated matches (864)

Protein domain: automated matches (864)

Rat (Rattus rattus) [TaxId: 10117] (1)

1a	d3b9kc2	C:108-214
1b	d3b9kl2	L:108-214

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

Protein domain: automated matches (311)

Rat (Rattus rattus) [TaxId: 10117] (1)

2a	d3b9kc1	C:1-107
2b	d3b9kl1	L:1-107

Protein domain: CD8 (10)

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

3a	d3b9ka_	A:
3b	d3b9ke_	E:

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

4a	d3b9kb_	B:
4b	d3b9kf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Rat (Rattus rattus) (1)

1a	3b9kC02	C:109-211
1b	3b9kL02	L:109-211
1c	3b9kC01	C:1-108
1d	3b9kL01	L:1-108
1e	3b9kD02	D:114-230
1f	3b9kH02	H:114-230
1g	3b9kD01	D:1-113
1h	3b9kH01	H:1-113
1i	3b9kA00	A:4-121
1j	3b9kE00	E:4-121

(no "Pfam Domain" information available for 3B9K)

Asymmetric Unit(hide GO term definitions)

Chain A,E (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,F (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.

Chain C,L (KACA_RAT | P01836)

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:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	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:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.

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	3b9k
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	KACA_RAT \| P01836
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	CD8A_MOUSE \| P01731	:	1bqh 1nez 2arj 2atp 3dmm
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(no "Related Entries Specified in the PDB File" available for 3B9K)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (9, 9)

Cis Peptide Bonds (14, 14)

Sequence-Structure Mapping

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PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (4, 8)

CATH Domains (1, 10)

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Gene Ontology (26, 46)

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Related Entries Specified in the PDB File