1R5V - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   EVIDENCE THAT STRUCTURAL REARRANGEMENTS AND/OR FLEXIBILITY DURING TCR BINDING CAN CONTRIBUTE TO T-CELL ACTIVATION

Authors :   M. Krogsgaard, N. Prado, E. J. Adams, X. L. He, D. C. Chow, D. B. Wilson, K. M. M. Davis

Date :   13 Oct 03 (Deposition) - 03 Feb 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (1x)
Biol. Unit 2: A,B,E  (1x)
Biol. Unit 3: C,D,F  (1x)

Keywords :   Tcr, Mhc Class Ii, Structural Rearangement, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Krogsgaard, N. Prado, E. J. Adams, X. L. He, D. C. Chow, D. B. Wilson, K. C. Garcia, M. M. Davis
Evidence That Structural Rearrangements And/Or Flexibility During Tcr Binding Can Contribute To T Cell Activation.
Mol. Cell V. 12 1367 2003
PubMed-ID: 14690592 | Reference-DOI: 10.1016/S1097-2765(03)00474-X

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEMEX-1
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ARTIFICIAL PEPTIDE
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	ARTIFICIAL
	Synthetic	:	YES

Molecule 3 - MHC H2-IE-BETA
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEMEX-1
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R5V)

(no "Site" information available for 1R5V)

Asymmetric Unit

No.	Residues
1	A:107	-	A:163
2	B:42	-	B:106
3	B:144	-	B:200
4	C:107	-	C:163
5	D:42	-	D:106
6	D:144	-	D:200

Asymmetric Unit

No.	Residues
1	Leu A:15	-	Pro A:16
2	Ser A:113	-	Pro A:114
3	Tyr B:150	-	Pro B:151
4	Leu C:15	-	Pro C:16
5	Ser C:113	-	Pro C:114
6	Tyr D:150	-	Pro D:151

(no "SAP(SNP)/Variant" information available for 1R5V)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA22_MOUSE	186-192	2	A:161-167 C:161-167
1	IG_MHC	PS00290		HB2I_MOUSE	198-204	2	B:198-204 D:198-204

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA22_MOUSE	186-192	2	A:161-167 C:161-167
1	IG_MHC	PS00290		HB2I_MOUSE	198-204	2	B:198-204 D:198-204

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA22_MOUSE	186-192	1	A:161-167 -
1	IG_MHC	PS00290		HB2I_MOUSE	198-204	1	B:198-204 -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA22_MOUSE	186-192	1	- C:161-167
1	IG_MHC	PS00290		HB2I_MOUSE	198-204	1	- D:198-204

(no "Exon" information available for 1R5V)

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:180
 aligned with HA22_MOUSE | P04224 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:180
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
           HA22_MOUSE    28 EEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 207
               SCOP domains d1r5va2 A:3-81 Class II MHC alpha chain, N-terminal domain                     d1r5va1 A:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains 1r5vA01 A:3-81                                                                 1r5vA02 A:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r5v A   3 EEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with HB2I_MOUSE | P18468 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:185
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
           HB2I_MOUSE    31 RPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
               SCOP domains d1r5vb2 B:31-120 Class II MHC beta chain, N-terminal domain                               d1r5vb1 B:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1r5vB01 B:31-119 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1r5vB02 B:120-215 Immunoglobulins                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhheeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.........eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee........eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5v B  31 APWFLEYSKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:180
 aligned with HA22_MOUSE | P04224 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:180
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
           HA22_MOUSE    28 EEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 207
               SCOP domains d1r5vc2 C:3-81 Class II MHC alpha chain, N-terminal domain                     d1r5vc1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains 1r5vC01 C:3-81                                                                 1r5vC02 C:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r5v C   3 EEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain D from PDB  Type:PROTEIN  Length:185
 aligned with HB2I_MOUSE | P18468 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:185
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
           HB2I_MOUSE    31 RPWFLEYCKSECHFYNGTQRVRFLKRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEILDEKRAAVDTYCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
               SCOP domains d1r5vd2 D:31-120 Class II MHC beta chain, N-terminal domain                               d1r5vd1 D:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1r5vD01 D:31-119 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1r5vD02 D:120-215 Immunoglobulins                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.hhheeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.........eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee........eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5v D  31 APWFLEYSKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain E from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .ee.......... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1r5v E   2 ADLIAYPKAATKF  14
                                    11

Chain F from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .ee.......... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1r5v F   2 ADLIAYPKAATKF  14
                                    11

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(

)

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)

House mouse (Mus musculus) (25)

1a	1r5vB01	B:31-119
1b	1r5vD01	D:31-119
1c	1r5vA01	A:3-81
1d	1r5vC01	C:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1r5vA02	A:82-181
2b	1r5vC02	C:82-181
2c	1r5vB02	B:120-215
2d	1r5vD02	D:120-215

(no "Pfam Domain" information available for 1R5V)

Asymmetric Unit(hide GO term definitions)

Chain A,C (HA22_MOUSE | P04224)

biological process
	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: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: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.
cellular component
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D (HB2I_MOUSE | P18468)

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: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: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:0034341	response to interferon-gamma	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-gamma stimulus. Interferon-gamma is also known as type II interferon.
cellular component
	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: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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1r5v)

	Sites
(no "Sites" information available for 1r5v)

	Cis Peptide Bonds
		Leu A:15 - Pro A:16	[ RasMol ]
		Leu C:15 - Pro C:16	[ RasMol ]
		Ser A:113 - Pro A:114	[ RasMol ]
		Ser C:113 - Pro C:114	[ RasMol ]
		Tyr B:150 - Pro B:151	[ RasMol ]
		Tyr D:150 - Pro D:151	[ RasMol ]

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	1r5v
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	HB2I_MOUSE \| P18468
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	HA22_MOUSE \| P04224	:	1fne 1fng 1i3r 1r5w 3qib 3qiu 3qiw 4p2o 4p2q 4p2r

(no "Related Entries Specified in the PDB File" available for 1R5V)

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

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