Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3O4L

Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000139	cellular_component	Golgi membrane
B	0001913	biological_process	T cell mediated cytotoxicity
B	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
B	0002237	biological_process	response to molecule of bacterial origin
B	0002376	biological_process	immune system process
B	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
B	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
B	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
B	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
B	0002726	biological_process	positive regulation of T cell cytokine production
B	0005198	molecular_function	structural molecule activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005765	cellular_component	lysosomal membrane
B	0005783	cellular_component	endoplasmic reticulum
B	0005788	cellular_component	endoplasmic reticulum lumen
B	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0005925	cellular_component	focal adhesion
B	0006826	biological_process	iron ion transport
B	0006879	biological_process	intracellular iron ion homeostasis
B	0006955	biological_process	immune response
B	0007608	biological_process	sensory perception of smell
B	0007611	biological_process	learning or memory
B	0009897	cellular_component	external side of plasma membrane
B	0009986	cellular_component	cell surface
B	0010038	biological_process	response to metal ion
B	0010977	biological_process	negative regulation of neuron projection development
B	0012507	cellular_component	ER to Golgi transport vesicle membrane
B	0016020	cellular_component	membrane
B	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
B	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
B	0023026	molecular_function	MHC class II protein complex binding
B	0030670	cellular_component	phagocytic vesicle membrane
B	0031901	cellular_component	early endosome membrane
B	0031902	cellular_component	late endosome membrane
B	0031905	cellular_component	early endosome lumen
B	0033077	biological_process	T cell differentiation in thymus
B	0033572	biological_process	transferrin transport
B	0034756	biological_process	regulation of iron ion transport
B	0034757	biological_process	negative regulation of iron ion transport
B	0035580	cellular_component	specific granule lumen
B	0042026	biological_process	protein refolding
B	0042605	molecular_function	peptide antigen binding
B	0042612	cellular_component	MHC class I protein complex
B	0042613	cellular_component	MHC class II protein complex
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0042824	cellular_component	MHC class I peptide loading complex
B	0045646	biological_process	regulation of erythrocyte differentiation
B	0048260	biological_process	positive regulation of receptor-mediated endocytosis
B	0048261	biological_process	negative regulation of receptor-mediated endocytosis
B	0050680	biological_process	negative regulation of epithelial cell proliferation
B	0050768	biological_process	negative regulation of neurogenesis
B	0050778	biological_process	positive regulation of immune response
B	0050870	biological_process	positive regulation of T cell activation
B	0051289	biological_process	protein homotetramerization
B	0055038	cellular_component	recycling endosome membrane
B	0060586	biological_process	multicellular organismal-level iron ion homeostasis
B	0070062	cellular_component	extracellular exosome
B	0071281	biological_process	cellular response to iron ion
B	0071283	biological_process	cellular response to iron(III) ion
B	0071316	biological_process	cellular response to nicotine
B	1904724	cellular_component	tertiary granule lumen
B	1990000	biological_process	amyloid fibril formation
B	1990712	cellular_component	HFE-transferrin receptor complex
B	2000774	biological_process	positive regulation of cellular senescence
B	2000978	biological_process	negative regulation of forebrain neuron differentiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 277

Chain	Residue
A	ARG35
A	HOH336
D	LYS148

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 278

Chain	Residue
A	LYS127
A	GLU128
A	ASP129

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 279

Chain	Residue
A	THR142
A	HIS145
A	LYS146

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 280

Chain	Residue
A	ARG131
A	ARG219
A	ARG256
E	ARG207

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 281

Chain	Residue
A	GLU232
A	THR233
A	LYS243
A	HOH295

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MES B 100

Chain	Residue
B	SER57
B	LYS58
B	ASP59

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 101

Chain	Residue
B	GLN2
B	ARG3
B	THR4

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 102

Chain	Residue
A	ARG21
B	HIS51
B	HOH169

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 103

Chain	Residue
B	ASN17
B	GLU74
B	ARG97

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 6

Chain	Residue
D	SER127
D	SER131
D	HOH205

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL D 202

Chain	Residue
C	THR4
D	ASP27
D	SER29
D	SER30
D	THR31
D	ASP93
D	ASN94
D	ASN95

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL E 1

Chain	Residue
E	ARG112
E	LEU113
E	THR114
E	PRO154
E	ASP155
E	TYR190

site_id	BC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL E 247

Chain	Residue
C	THR4
C	LEU5
C	VAL6
D	TYR34
D	ASP93
D	ALA96
E	ARG98
E	GLY102
E	ASN103
E	TYR105

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL E 248

Chain	Residue
E	SER220
E	ASN222
E	ASP223
E	HOH345

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL E 249

Chain	Residue
E	PHE29
E	GLN30
E	GLY100
E	HOH264

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 250

Chain	Residue
E	TRP11
E	VAL12
E	ILE13
E	HIS156
E	TYR217
E	GLY218
E	HOH272

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 E 251

Chain	Residue
E	GLU167
E	VAL168
E	HIS169
E	SER170
E	HOH323
E	HOH338

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 252

Chain	Residue
D	LYS130
E	THR150
E	GLU181

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 253

Chain	Residue
E	HIS8
E	PRO9
E	SER10

Functional Information from PROSITE/UniProt

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YACRVNH

Chain	Residue	Details
B	TYR78-HIS84
A	TYR257-HIS263

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI2
Number of Residues	88
Details	Domain: {"description":"Ig-like C1-type"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Modified residue: {"description":"Pyrrolidone carboxylic acid; in form pI 5.3","evidences":[{"source":"PubMed","id":"7554280","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Glycosylation: {"description":"N-linked (Glc) (glycation) isoleucine; in hemodialysis-associated amyloidosis","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Glycosylation: {"description":"N-linked (Glc) (glycation) lysine; in vitro","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PROSITE-ProRule","id":"PRU00498","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19349973","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PROSITE-ProRule","id":"PRU00498","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	109
Details	Domain: {"description":"Ig-like C1-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00114","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)