3L6F - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURE OF MHC CLASS II MOLECULE HLA-DR1 COMPLEXED WITH PHOSPHOPEPTIDE MART-1

Authors :   Y. Li, R. A. Mariuzza

Date :   23 Dec 09 (Deposition) - 12 May 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Mhc Class Ii, Hla-Dr1, Phosphopeptide, Disulfide Bond, Glycoprotein, Immune Response, Membrane, Mhc Ii, Transmembrane, Endoplasmic Reticulum, Golgi Apparatus, Immune System-Peptide Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Li, F. R. Depontieu, J. Sidney, T. M. Salay, V. H. Engelhard, D. F. Hunt, A. Sette, S. L. Topalian, R. A. Mariuzza
Structural Basis For The Presentation Of Tumor-Associated Mhc Class Ii-Restricted Phosphopeptides To Cd4(+) T Cells.
J. Mol. Biol. V. 399 596 2010
PubMed-ID: 20417641 | Reference-DOI: 10.1016/J.JMB.2010.04.037

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET-26B
	Fragment	:	UNP RESIDUES 26-207
	Gene	:	HLA-DRA, HLA-DRA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS II ANTIGEN DRA

Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 30-221
	Gene	:	HLA-DRB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS I ANTIGEN DRB1*1, DR-1, DR1

Molecule 3 - MELANOMA ANTIGEN RECOGNIZED BY T-CELLS 1
	Chains	:	C
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 100-114
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MART-1, MELAN-A PROTEIN, ANTIGEN SK29-AA, ANTIGEN LB39-AA
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

(no "Site" information available for 3L6F)

Asymmetric/Biological Unit

No.	Residues
1	A:107	-	A:163
2	B:15	-	B:79
3	B:117	-	B:173

Asymmetric/Biological Unit

No.	Residues
1	Asn A:15	-	Pro A:16
2	Thr A:113	-	Pro A:114
3	Tyr B:123	-	Pro B:124

Asymmetric/Biological Unit (26, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_033378	A	29	S	2B11_HUMAN	Polymorphism	9270299	B	M	0	S
02	UniProt	VAR_033379	R	33	K	2B11_HUMAN	Polymorphism	34716432	B	R	4	K
03	UniProt	VAR_033380	R	33	Q	2B11_HUMAN	Polymorphism	34716432	B	R	4	Q
04	UniProt	VAR_016740	Q	39	E	2B11_HUMAN	Polymorphism	---	B	Q	10	E
05	UniProt	VAR_033381	S	66	Y	2B11_HUMAN	Polymorphism	16822820	B	S	37	Y
06	UniProt	VAR_016741	G	74	R	2B11_HUMAN	Polymorphism	---	B	G	45	R
07	UniProt	VAR_033382	Y	76	F	2B11_HUMAN	Polymorphism	1060346	B	Y	47	F
08	UniProt	VAR_033383	Y	89	S	2B11_HUMAN	Polymorphism	36074728	B	Y	60	S
09	UniProt	VAR_016710	L	96	I	2B11_HUMAN	Polymorphism	---	B	L	67	I
10	UniProt	VAR_016711	Q	99	D	2B11_HUMAN	Polymorphism	---	B	Q	70	D
11	UniProt	VAR_033384	Q	99	E	2B11_HUMAN	Polymorphism	17881965	B	Q	70	E
12	UniProt	VAR_033385	Q	99	H	2B11_HUMAN	Polymorphism	17879599	B	Q	70	H
13	UniProt	VAR_016742	R	100	A	2B11_HUMAN	Polymorphism	---	B	R	71	A
14	UniProt	VAR_016712	R	100	E	2B11_HUMAN	Polymorphism	---	B	R	71	E
15	UniProt	VAR_033386	A	102	G	2B11_HUMAN	Polymorphism	17878857	B	A	73	G
16	UniProt	VAR_033387	A	103	E	2B11_HUMAN	Polymorphism	16822805	B	A	74	E
17	UniProt	VAR_016713	T	106	N	2B11_HUMAN	Polymorphism	16822752	B	T	77	N
18	UniProt	VAR_033388	Y	107	H	2B11_HUMAN	Polymorphism	16822512	B	Y	78	H
19	UniProt	VAR_016714	V	114	A	2B11_HUMAN	Polymorphism	17424145	B	V	85	A
20	UniProt	VAR_016715	G	115	V	2B11_HUMAN	Polymorphism	2230810	B	G	86	V
21	UniProt	VAR_033389	G	164	D	2B11_HUMAN	Polymorphism	1059633	B	G	135	D
22	UniProt	VAR_033390	A	169	T	2B11_HUMAN	Polymorphism	2308768	B	A	140	T
23	UniProt	VAR_033391	V	171	M	2B11_HUMAN	Polymorphism	701829	B	V	142	M
24	UniProt	VAR_033392	Q	178	H	2B11_HUMAN	Polymorphism	701830	B	Q	149	H
25	UniProt	VAR_033393	R	195	Q	2B11_HUMAN	Polymorphism	3205588	B	R	166	Q
26	UniProt	VAR_033394	T	210	I	2B11_HUMAN	Polymorphism	17423930	B	T	181	I

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

Asymmetric/Biological 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.	DRA_HUMAN	186-192	1	A:161-167
1	IG_MHC	PS00290		2B11_HUMAN	200-206	1	B:171-177

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.3	ENST00000360004	3	ENSE00001930619	chr6:32557625-32557420	206	2B11_HUMAN	1-34	34	1	B:0-5	6
1.4	ENST00000360004	4	ENSE00001731226	chr6:32552155-32551886	270	2B11_HUMAN	34-124	91	1	B:5-95	91
1.5b	ENST00000360004	5b	ENSE00001801024	chr6:32549615-32549334	282	2B11_HUMAN	124-218	95	1	B:95-189	95
1.6	ENST00000360004	6	ENSE00001717727	chr6:32548633-32548523	111	2B11_HUMAN	218-255	38	1	B:189-190	2
1.7	ENST00000360004	7	ENSE00001773376	chr6:32548047-32548024	24	2B11_HUMAN	255-263	9	0	-	-
1.8	ENST00000360004	8	ENSE00001954617	chr6:32546881-32546546	336	2B11_HUMAN	263-266	4	0	-	-

2.1a	ENST00000381477	1a	ENSE00001488744	chr9:5890802-5890936	135	MAR1_HUMAN	-	0	0	-	-
2.2a	ENST00000381477	2a	ENSE00001488741	chr9:5892450-5892551	102	MAR1_HUMAN	1-26	26	0	-	-
2.3a	ENST00000381477	3a	ENSE00000813180	chr9:5897557-5897653	97	MAR1_HUMAN	26-58	33	0	-	-
2.5a	ENST00000381477	5a	ENSE00000927858	chr9:5906885-5906998	114	MAR1_HUMAN	59-96	38	0	-	-
2.6c	ENST00000381477	6c	ENSE00001488710	chr9:5908640-5910606	1967	MAR1_HUMAN	97-118	22	1	C:1-15	15

3.6a	ENST00000383259	6a	ENSE00001839042	HSCHR6_MHC_QBL:32365090-32365280	191	DRA_HUMAN	1-28	28	1	A:3-3	1
3.7b	ENST00000383259	7b	ENSE00001719010	HSCHR6_MHC_QBL:32367694-32367939	246	DRA_HUMAN	28-110	83	1	A:3-85	83
3.8c	ENST00000383259	8c	ENSE00001737588	HSCHR6_MHC_QBL:32368431-32368712	282	DRA_HUMAN	110-204	95	1	A:85-179	95
3.9a	ENST00000383259	9a	ENSE00001770912	HSCHR6_MHC_QBL:32369002-32369167	166	DRA_HUMAN	204-254	51	1	A:179-180	2
3.10b	ENST00000383259	10b	ENSE00001925700	HSCHR6_MHC_QBL:32369906-32370300	395	DRA_HUMAN	-	0	0	-	-

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:178
 aligned with DRA_HUMAN | P01903 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:178
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197        
            DRA_HUMAN    28 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3l6fA01 A:3-81                                                                 3l6fA02 A:82-180 Immunoglobulins                                                                    CATH domains
               Pfam domains -MHC_II_alpha-3l6fA02 A:4-84                                                      --------C1-set-3l6fA01 A:93-175                                                            ----- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
           Transcript 3 (1) 3---------------------------------------------------------------------------------Exon 3.8c  PDB: A:85-179 UniProt: 110-204                                                      - Transcript 3 (1)
           Transcript 3 (2) Exon 3.7b  PDB: A:3-85 UniProt: 28-110                                             ---------------------------------------------------------------------------------------------3. Transcript 3 (2)
                 3l6f A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKQWEF 180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with 2B11_HUMAN | P04229 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:191
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218 
           2B11_HUMAN    29 AGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 219
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3l6fB01 B:0-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1          3l6fB02 B:93-190 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------MHC_II_beta-3l6fB02 B:13-87                                                ---------------C1-set-3l6fB01 B:103-185                                                           ----- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee. Sec.struct. author
             SAPs(SNPs) (1) S---K-----E--------------------------Y-------R-F------------S------I--DA-GE--NH------AV------------------------------------------------D----T-M------H----------------Q--------------I--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----Q-----------------------------------------------------------------EE----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ----------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
           Transcript 1 (1) 1.3   -----------------------------------------------------------------------------------------Exon 1.5b  PDB: B:95-189 UniProt: 124-218                                                      - Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.4  PDB: B:5-95 UniProt: 34-124                                                      ---------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 3l6f B   0 MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 190
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain C from PDB  Type:PROTEIN  Length:15
 aligned with MAR1_HUMAN | Q16655 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:15
                                   109     
           MAR1_HUMAN   100 APPAYEKLSAEQSPP 114
               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 2 Exon 2.6c       Transcript 2
                 3l6f C   1 APPAYEKLsAEQSPP  15
                                    10     
                                    9-SEP

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 '\|'

(no "SCOP Domain" information available for 3L6F)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Homologous Superfamily: Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 (75)

Human (Homo sapiens) (48)

1a	3l6fB01	B:0-92
1b	3l6fA01	A:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	3l6fA02	A:82-180
2b	3l6fB02	B:93-190

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Homo sapiens (Human) (218)

1a	C1-set-3l6fB01	B:103-185
1b	C1-set-3l6fA01	A:93-175

Clan: MHC (252)

Family: MHC_II_alpha (42)

Homo sapiens (Human) (26)

MHC_II_alpha-3l6fA02

A:4-84

Family: MHC_II_beta (39)

Homo sapiens (Human) (25)

MHC_II_beta-3l6fB02

B:13-87

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DRA_HUMAN | P01903)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	GO:0032395	MHC class II receptor activity	Combining with an MHC class II protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
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:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0050890	cognition	The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
	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: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:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0002503	peptide antigen assembly with MHC class II protein complex	The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
	GO:0002506	polysaccharide assembly with MHC class II protein complex	The binding of a polysaccharide to the antigen binding groove of an MHC class II protein complex.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.
	GO:0032588	trans-Golgi network membrane	The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

Chain B (2B11_HUMAN | P04229)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
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:0042088	T-helper 1 type immune response	An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0016045	detection of bacterium	The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
	GO:0002455	humoral immune response mediated by circulating immunoglobulin	An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.
	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: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:0002381	immunoglobulin production involved in immunoglobulin mediated immune response	The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels.
	GO:0002437	inflammatory response to antigenic stimulus	An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
	GO:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	GO:0032689	negative regulation of interferon-gamma production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0035774	positive regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0051262	protein tetramerization	The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
	GO:2001179	regulation of interleukin-10 secretion	Any process that modulates the frequency, rate or extent of interleukin-10 secretion.
	GO:0032673	regulation of interleukin-4 production	Any process that modulates the frequency, rate, or extent of interleukin-4 production.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0012507	ER to Golgi transport vesicle membrane	The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0030669	clathrin-coated endocytic vesicle membrane	The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
	GO:0030666	endocytic vesicle membrane	The lipid bilayer surrounding an endocytic vesicle.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0071556	integral component of lumenal side of endoplasmic reticulum membrane	The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
	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:0031902	late endosome membrane	The lipid bilayer surrounding a late endosome.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	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.
	GO:0032588	trans-Golgi network membrane	The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
	GO:0030658	transport vesicle membrane	The lipid bilayer surrounding a transport vesicle.

Chain C (MAR1_HUMAN | Q16655)

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).
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0042470	melanosome	A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005802	trans-Golgi network	The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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	3l6f
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	MAR1_HUMAN \| Q16655
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(no "Related Entries Specified in the PDB File" available for 3L6F)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (26, 26)

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Exons (9, 9)

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