1R5W - JenaLib

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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. Adams, X. He, D. C. Chow, D. B. Wilson, K. C. Ga M. M. Davis

Date :   13 Oct 03 (Deposition) - 02 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (1x)
Biol. Unit 2: C,D,F  (1x)
Biol. Unit 3: A,B,E  (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 - 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
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - ARTIFICIAL PEPTIDE
	Chains	:	E, F
	Engineered	:	YES
	Other Details	:	ARTIFICIAL
	Synthetic	:	YES

		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)	:			C	D		F
Biological Unit 3 (1x)	:	A	B			E

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1R5W)

(no "Site" information available for 1R5W)

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 1R5W)

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.	HA22_MOUSE	186-192	2	A:161-167 C:161-167

Biological Unit 1 (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	2	A:161-167 C:161-167

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.	HA22_MOUSE	186-192	1	- C:161-167

Biological Unit 3 (1, 1)

	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 -

(no "Exon" information available for 1R5W)

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 d1r5wa2 A:3-81 Class II MHC alpha chain, N-terminal domain                     d1r5wa1 A:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains 1r5wA01 A:3-81                                                                 1r5wA02 A:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeee....eeeeeee...eeeeee....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r5w 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 Q31164_MOUSE | Q31164 from UniProtKB/TrEMBL  Length:237

    Alignment length:185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
         Q31164_MOUSE     4 RPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
               SCOP domains d1r5wb2 B:31-120 Class II MHC beta chain, N-terminal domain                               d1r5wb1 B:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1r5wB01 B:31-119 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1r5wB02 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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5w 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 d1r5wc2 C:3-81 Class II MHC alpha chain, N-terminal domain                     d1r5wc1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains 1r5wC01 C:3-81                                                                 1r5wC02 C:82-181 Immunoglobulins                                                                    - CATH domains
           Pfam domains (1) -MHC_II_alpha-1r5wC03 C:4-84                                                      --------C1-set-1r5wC01 C:93-175                                                            ------- Pfam domains (1)
           Pfam domains (2) -MHC_II_alpha-1r5wC04 C:4-84                                                      --------C1-set-1r5wC02 C:93-175                                                            ------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeee....eeeeeee...eeeeee....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r5w 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 Q31164_MOUSE | Q31164 from UniProtKB/TrEMBL  Length:237

    Alignment length:185
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183     
         Q31164_MOUSE     4 RPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
               SCOP domains d1r5wd2 D:31-120 Class II MHC beta chain, N-terminal domain                               d1r5wd1 D:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1r5wD01 D:31-119 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1r5wD02 D:120-215 Immunoglobulins                                                                CATH domains
           Pfam domains (1) ---------MHC_II_beta-1r5wD03 D:40-114                                               ---------------C1-set-1r5wD01 D:130-212                                                           --- Pfam domains (1)
           Pfam domains (2) ---------MHC_II_beta-1r5wD04 D:40-114                                               ---------------C1-set-1r5wD02 D:130-212                                                           --- Pfam domains (2)
         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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r5w 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 ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1r5w E   2 ADLIAYFKAATKF  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 ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 1r5w F   2 ADLIAYFKAATKF  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	1r5wB01	B:31-119
1b	1r5wD01	D:31-119
1c	1r5wA01	A:3-81
1d	1r5wC01	C:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1r5wA02	A:82-181
2b	1r5wC02	C:82-181
2c	1r5wB02	B:120-215
2d	1r5wD02	D:120-215

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

1a	C1-set-1r5wC01	C:93-175
1b	C1-set-1r5wC02	C:93-175
1c	C1-set-1r5wD01	D:130-212
1d	C1-set-1r5wD02	D:130-212

Clan: MHC (252)

Family: MHC_II_alpha (42)

Mus musculus (Mouse) (16)

2a	MHC_II_alpha-1r5wC03	C:4-84
2b	MHC_II_alpha-1r5wC04	C:4-84

Family: MHC_II_beta (39)

Mus musculus (Mouse) (14)

3a	MHC_II_beta-1r5wD03	D:40-114
3b	MHC_II_beta-1r5wD04	D:40-114

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 (Q31164_MOUSE | Q31164)

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.

Asymmetric Unit
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(no "Ligands, Modified Residues, Ions" information available for 1r5w)

	Sites
(no "Sites" information available for 1r5w)

	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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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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	Q31164_MOUSE \| Q31164
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UniProtKB/Swiss-Prot
	HA22_MOUSE \| P04224	:	1fne 1fng 1i3r 1r5v 3qib 3qiu 3qiw 4p2o 4p2q 4p2r
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	Q31164_MOUSE \| Q31164	:	1ieb

(no "Related Entries Specified in the PDB File" available for 1R5W)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (4, 8)

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