1IEA - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HISTOCOMPATIBILITY ANTIGEN

Authors :   D. H. Fremont, W. A. Hendrickson, P. Marrack, J. Kappler

Date :   05 Apr 96 (Deposition) - 05 Jun 97 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Histocompatibility Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Fremont, W. A. Hendrickson, P. Marrack, J. Kappler
Structures Of An Mhc Class Ii Molecule With Covalently Boun Single Peptides.
Science V. 272 1001 1996
PubMed-ID: 8638119

Molecule 1 - MHC CLASS II I-EK
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	WITH COVALENTLY BOUND HB PEPTIDE

Molecule 2 - MHC CLASS II I-EK
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	WITH COVALENTLY BOUND HB PEPTIDE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:78	BINDING SITE FOR RESIDUE NAG A 193
2	AC2	SOFTWARE	ASN A:118 , ASP A:166 , HIS A:167 , TRP A:168	BINDING SITE FOR RESIDUE NAG A 194
3	AC3	SOFTWARE	ILE A:1 , THR A:157 , ASN B:19 , GLN B:22	BINDING SITE FOR RESIDUE NAG B 199
4	AC4	SOFTWARE	ASN C:78	BINDING SITE FOR RESIDUE NAG C 193
5	AC5	SOFTWARE	ASN C:118 , HIS C:167 , TRP C:168 , HOH C:204	BINDING SITE FOR RESIDUE NAG C 194
6	AC6	SOFTWARE	GLU A:171 , ILE C:1 , ASN D:19 , GLN D:22 , HOH D:271	BINDING SITE FOR RESIDUE NAG D 199

Asymmetric Unit

No.	Residues
1	A:107	-	A:163
2	B:15	-	B:79
3	B:117	-	B:173
4	C:107	-	C:163
5	D:15	-	D:79
6	D:117	-	D:173

Asymmetric Unit

No.	Residues
1	Leu A:15	-	Pro A:16
2	Ser A:113	-	Pro A:114
3	Tyr B:123	-	Pro B:124
4	Leu C:15	-	Pro C:16
5	Ser C:113	-	Pro C:114
6	Tyr D:123	-	Pro D:124

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

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.	HA21_MOUSE	186-192	2	A:161-167 C:161-167

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	HA21_MOUSE	186-192	1	A: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.	HA21_MOUSE	186-192	1	- C:161-167

(no "Exon" information available for 1IEA)

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:182
 aligned with HA21_MOUSE | P01904 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:182
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  
           HA21_MOUSE    26 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKTWEFEE 207
               SCOP domains d1ieaa2 A:1-81 Class II MHC alpha chain, N-terminal domain                       d1ieaa1 A:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1ieaA01 A:3-81                                                                 1ieaA02 A:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee..hhhhh.....hhhhhhhhhhhhhhhhhhhhh...........eeeeee........eeeeeeeee.......eeeeee........eee............eeeeeeee.....eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iea A   1 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKTWEFEE 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:214
 aligned with Q31163_MOUSE | Q31163 from UniProtKB/TrEMBL  Length:263

    Alignment length:214
                                       17   18                                                                                                                                                                                                    
                                    14  |    |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
         Q31163_MOUSE     5 RVPCVAAVILLLT----VLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 214
               SCOP domains -----------------------------d1ieab2 B:4-92 Class II MHC beta chain, N-terminal domain                                d1ieab1 B:93-188 Class II MHC beta chain, C-terminal domain                                      SCOP domains
               CATH domains -------------------------------1ieaB01 B:6-93 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1     1ieaB02 B:94-188 Immunoglobulins                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee.............eeeeeeeeeee......eeeeeeeee..eeeeeee....eeee..hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh.........eeeeeee........eeeeeeeeee....eeeeeee........eee..........eeeeeeeee.......eeeeeee......eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iea B  5N GKKVITAFNEGLKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
                            ||||||||6P||||||||7L|||||||||4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                           5N|||||||6P|||||||6L||||||15L||                                                                                                                                                                                        
                            6N|||||||7P|||||||7L||||||16L|                                                                                                                                                                                        
                             7N|||||| 8P|||||| 8L||||||  4                                                                                                                                                                                        
                              8N|||||  9P|||||  9L|||||                                                                                                                                                                                           
                               1P||||   1L||||  10L||||                                                                                                                                                                                           
                                2P|||    2L|||   11L|||                                                                                                                                                                                           
                                 3P||     3L||    12L||                                                                                                                                                                                           
                                  4P|      4L|     13L|                                                                                                                                                                                           
                                   5P       5L      14L

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with HA21_MOUSE | P01904 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:182
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  
           HA21_MOUSE    26 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKTWEFEE 207
               SCOP domains d1ieac2 C:1-81 Class II MHC alpha chain, N-terminal domain                       d1ieac1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1ieaC01 C:3-81                                                                 1ieaC02 C:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee..hhhhh.eee.hhhhhhhhhhhhhhhhhhhhh...........eeeeee........eeeeeeeee.......eeeeee........eee............eeeeeeee.....eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iea C   1 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKTWEFEE 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with Q31163_MOUSE | Q31163 from UniProtKB/TrEMBL  Length:263

    Alignment length:214
                                       17   18                                                                                                                                                                                                    
                                    14  |    |20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
         Q31163_MOUSE     5 RVPCVAAVILLLT----VLSPPVALVRDSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 214
               SCOP domains -----------------------------d1iead2 D:4-92 Class II MHC beta chain, N-terminal domain                                d1iead1 D:93-188 Class II MHC beta chain, C-terminal domain                                      SCOP domains
               CATH domains -------------------------------1ieaD01 D:6-93 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1     1ieaD02 D:94-188 Immunoglobulins                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...........................eeeeeeeeeee......eeeeeeeee..eeeeeee....eeee..hhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh.........eeeeeee........eeeeeeee......eeeeeee..eee...eee............eeeeeee.......eeeeeee......eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iea D  5N GKKVITAFNEGLKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
                            ||||||||6P||||||||7L|||||||||4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
                           5N|||||||6P|||||||6L||||||15L||                                                                                                                                                                                        
                            6N|||||||7P|||||||7L||||||16L|                                                                                                                                                                                        
                             7N|||||| 8P|||||| 8L||||||  4                                                                                                                                                                                        
                              8N|||||  9P|||||  9L|||||                                                                                                                                                                                           
                               1P||||   1L||||  10L||||                                                                                                                                                                                           
                                2P|||    2L|||   11L|||                                                                                                                                                                                           
                                 3P||     3L||    12L||                                                                                                                                                                                           
                                  4P|      4L|     13L|                                                                                                                                                                                           
                                   5P       5L      14L

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	1ieaB01	B:6-93
1b	1ieaD01	D:6-93
1c	1ieaA01	A:3-81
1d	1ieaC01	C:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1ieaA02	A:82-181
2b	1ieaC02	C:82-181
2c	1ieaB02	B:94-188
2d	1ieaD02	D:94-188

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (HA21_MOUSE | P01904)

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 (Q31163_MOUSE | Q31163)

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.

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	HA21_MOUSE \| P01904	:	1ieb 1kt2 1ktd
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	Q31163_MOUSE \| Q31163	:	4p2o 4p2q 4p2r

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

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 6)

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SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

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