3B9K | pdb_00003b9k

Crystal structure of CD8alpha-beta in complex with YTS 156.7 FAB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth F]	d3b9kf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD8	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d3b9kb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD8	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth E]	d3b9ke_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD8	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d3b9ka_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD8	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth D]	d3b9kd_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)
B [auth H]	d3b9kh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)
E [auth C]	d3b9kc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)
E [auth C]	d3b9kc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)
A [auth L]	d3b9kl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)
A [auth L]	d3b9kl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Rattus rattus ) [TaxId: 10117 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth F]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054491	3000071	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054491	3000071	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054489	3000071	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054489	3000071	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth F]	HSP70	e3b9kF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
D [auth B]	Acyl_transf_1	e3b9kB1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Acyl_transf_1	ECOD (v294.1)
G [auth E]	HSP70	e3b9kE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
C [auth A]	Acyl_transf_1	e3b9kA1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Acyl_transf_1	ECOD (v294.1)
F [auth D]	HSP70	e3b9kD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
B [auth H]	CRISPR_Cas2	e3b9kH1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: CRISPR_Cas2	ECOD (v294.1)
E [auth C]	HSP70	e3b9kC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HSP70	ECOD (v294.1)
A [auth L]	CRISPR_Cas2	e3b9kL1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: CRISPR_Cas2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
D [auth B], H [auth F]	CD8A_CD8B heterodimer	1V-LIKE	Mus musculus (house mouse)	CD8B*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE_1V-LIKE	IMGT (202611-0)
C [auth A], G [auth E]	CD8A_CD8B heterodimer	1V-LIKE	Mus musculus (house mouse)	CD8A*02	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE_1V-LIKE	IMGT (202611-0)
B [auth H], F [auth D]	Fab YTS 156.7.7	VH-CH1	Rattus norvegicus (Norway rat)	IGHV2-101, IGHJ201, IGHG2B*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202611-0)
A [auth L], E [auth C]	Fab YTS 156.7.7	L-KAPPA	Rattus norvegicus (Norway rat)	IGKV19S201, IGKJ2-301, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], F [auth D]	Heavy Chain	IGHV2	-	t-cell surface glycoprotein cd8 beta chain	SAbDab (2026-03-27)
A [auth L], E [auth C]	Light Chain	IGKV19	Kappa	t-cell surface glycoprotein cd8 beta chain	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth B], H [auth F]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth A], G [auth E]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B [auth H], F [auth D]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A [auth L], E [auth C]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth B], H [auth F]	T-cell surface glycoprotein CD8 beta chain	molecular transducer activity coreceptor activity signaling receptor activity protein binding binding MHC class I protein binding signaling receptor binding MHC protein binding	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response biological regulation T cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response	protein-containing complex receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane
C [auth A], G [auth E]	T-cell surface glycoprotein CD8 alpha chain	protein binding binding kinase binding enzyme binding protein kinase binding protein-containing complex binding MHC protein complex binding MHC class I protein complex binding identical protein binding	multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process multicellular organismal process T cell activation immune system process cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication positive regulation of signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity immune response leukocyte mediated immunity adaptive immune response immune effector process cell surface receptor signaling pathway immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response developmental process cytotoxic T cell differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation cell differentiation anatomical structure development T cell differentiation leukocyte differentiation biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	protein-containing complex receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane microdomain membrane raft plasma membrane raft plasma membrane region
B [auth H], F [auth D]	Fab Heavy chain	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	humoral immune response biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress immune system process humoral immune response biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response immune response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress immune system process response to bacterium response to external biotic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus B cell mediated immunity regulation of immune response activation of immune response	protein-containing complex cellular anatomical structure extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex
A [auth L], E [auth C]	Fab Light Chain	-	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation response to stimulus immune response adaptive immune response	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex alpha-beta T cell receptor complex receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex T cell receptor complex IgG immunoglobulin complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth B], H [auth F]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth B], H [auth F]	IPR042414	T-cell surface glycoprotein CD8 beta chain	Family
D [auth B], H [auth F]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth B], H [auth F]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth B], H [auth F]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth B], H [auth F]	IPR007110	Immunoglobulin-like domain	Domain
C [auth A], G [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth A], G [auth E]	IPR015468	CD8 alpha subunit	Family
C [auth A], G [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A], G [auth E]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth A], G [auth E]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth A], G [auth E]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H], F [auth D]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H], F [auth D]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H], F [auth D]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H], F [auth D]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H], F [auth D]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H], F [auth D]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth L], E [auth C]	IPR003597	Immunoglobulin C1-set	Domain
A [auth L], E [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L], E [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L], E [auth C]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L], E [auth C]	IPR050380	Immune Recognition and Response Modulators	Family
A [auth L], E [auth C]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site