1FNE - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   HISTOCOMPATIBILITY ANTIGEN

Authors :   M. J. Miley, C. A. Nelson, D. H. Fremont

Date :   21 Aug 00 (Deposition) - 07 Mar 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   G. J. Kersh, M. J. Miley, C. A. Nelson, A. Grakoui, S. Horvath, D. L. Donermeyer, J. Kappler, P. M. Allen, D. H. Fremont
Structural And Functional Consequences Of Altering A Peptid Mhc Anchor Residue.
J. Immunol. V. 166 3345 2001
PubMed-ID: 11207290

Molecule 1 - PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	SOLUBLE ECTO-DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	SOLUBLE ECTO-DOMAIN WITH COVALENTLY ATTACHED HB PEPTIDE
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	WITH COVALENTLY BOUND HB(D73) PEPTIDE

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

Biological Unit 3 (1, 12)

No.	Name	Count	Type	Full Name
1	NAG	12	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 601
2	AC2	SOFTWARE	ASN A:118 , ASP A:166 , TRP A:168 , HOH A:738	BINDING SITE FOR RESIDUE NAG A 602
3	AC3	SOFTWARE	ILE A:1 , THR A:157 , ASN B:19 , GLN B:22 , HOH B:661	BINDING SITE FOR RESIDUE NAG B 603
4	AC4	SOFTWARE	ASN C:78 , HOH C:732	BINDING SITE FOR RESIDUE NAG C 604
5	AC5	SOFTWARE	ASN C:118 , ASP C:166 , TRP C:168	BINDING SITE FOR RESIDUE NAG C 605
6	AC6	SOFTWARE	GLU A:171 , ILE C:1 , LYS C:2 , GLY D:14L , ASN D:19 , HOH D:694	BINDING SITE FOR RESIDUE NAG D 606

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 1FNE)

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, 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 -

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, 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	4	A:161-167 C:161-167

(no "Exon" information available for 1FNE)

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 HA22_MOUSE | P04224 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  
           HA22_MOUSE    26 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 207
               SCOP domains d1fnea2 A:1-81 Class II MHC alpha chain, N-terminal domain                       d1fnea1 A:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1fneA01 A:3-81                                                                 1fneA02 A:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fne A   1 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 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:213
                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------d1fneb2 B:4-92 Class II MHC beta chain, N-terminal domain                                d1fneb1 B:93-188 Class II MHC beta chain, C-terminal domain                                      SCOP domains
               CATH domains ------------------------------1fneB01 B:6-93 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1     1fneB02 B:94-188 Immunoglobulins                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee.............eeeeeeeeeee.hhhh.eeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.........eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee........eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fne B  6N KKVITAFNDGLKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
                            ||||||||7P||||||||8L|||||||||5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   
                           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|                                                                                                                                                                                          
                                   6P       6L      15L

Chain C from PDB  Type:PROTEIN  Length:182
 aligned with HA22_MOUSE | P04224 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  
           HA22_MOUSE    26 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 207
               SCOP domains d1fnec2 C:1-81 Class II MHC alpha chain, N-terminal domain                       d1fnec1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1fneC01 C:3-81                                                                 1fneC02 C:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fne C   1 IKEEHTIIQAEFYLLPDKRGEFMFDFDGDEIFHVDIEKSETIWRLEEFAKFASFEAQGALANIAVDKANLDVMKERSNNTPDANVAPEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVDHWGLEEPLRKHWEFEE 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:213
                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------d1fned2 D:4-92 Class II MHC beta chain, N-terminal domain                                d1fned1 D:93-188 Class II MHC beta chain, C-terminal domain                                      SCOP domains
               CATH domains ------------------------------1fneD01 D:6-93 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1     1fneD02 D:94-188 Immunoglobulins                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee............eee.............eeeeeeeeeeeeehhheeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee.........eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee........eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fne D  6N KKVITAFNDGLKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 188
                            ||||||||7P||||||||8L|||||||||5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   
                           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|                                                                                                                                                                                          
                                   6P       6L      15L

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	1fneB01	B:6-93
1b	1fneD01	D:6-93
1c	1fneA01	A:3-81
1d	1fneC01	C:3-81

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1fneA02	A:82-181
2b	1fneC02	C:82-181
2c	1fneB02	B:94-188
2d	1fneD02	D:94-188

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

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.

Asymmetric Unit
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	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:123 - Pro B:124	[ RasMol ]
		Tyr D:123 - Pro D:124	[ RasMol ]

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	1fne
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	HBB2_MOUSE \| P02089
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UniProtKB/Swiss-Prot
	HA22_MOUSE \| P04224	:	1fng 1i3r 1r5v 1r5w 3qib 3qiu 3qiw 4p2o 4p2q 4p2r
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1iea	INITIAL I-EK/HB STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 8)

CATH Domains (2, 8)

Pfam Domains (0, 0)

Gene Ontology (18, 18)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File