1KTD - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON CYTOCHROME C PEPTIDE

Authors :   D. H. Fremont, S. Dai, H. Chiang, F. Crawford, P. Marrack, J. Kappler

Date :   15 Jan 02 (Deposition) - 01 May 02 (Release) - 21 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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  (1x)

Keywords :   Protein-Peptide Complex, T Cell Receptor, Antigen Presentation, Cytochrome, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Fremont, S. Dai, H. Chiang, F. Crawford, P. Marrack, J. Kappler
Structural Basis Of Cytochrome C Presentation By Ie(K).
J. Exp. Med. V. 195 1043 2002
PubMed-ID: 11956295 | Reference-DOI: 10.1084/JEM.20011971

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-D ALPHA CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Gene	:	H2-EA
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	H2-IE-ALPHA

Molecule 2 - FUSION PROTEIN CONSISTING OF CYTOCHROME C PEPTIDE, GLYCINE RICH LINKER, AND MHC E-BETA-K
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Cell Line	:	SF9
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Gene	:	CYC, H2-EB1
	Mutation	:	YES
	Organism Common	:	ROCK DOVE, MOUSE
	Organism Scientific	:	COLUMBA LIVIA, MUS MUSCULUS
	Organism Taxid	:	8932, 10090
	Other Details	:	FUSION PROTEIN CONSISTS OF PIGEON CYTOCHROME C PEPTIDE, RESIDUES 1-14 (AADLIAYLKQASAK), GLYCINE RICH LINKER, RESIDUES 15-30 (GGGGSLVGGGSGGGGS) AND MOUSE MHC E-BETA-K CHAIN

		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 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:1 , ASN B:46 , GLN B:49	BINDING SITE FOR RESIDUE NAG B 601
2	AC2	SOFTWARE	ASN A:78 , VAL B:21	BINDING SITE FOR RESIDUE NAG A 602
3	AC3	SOFTWARE	ASN C:78 , GLY D:22	BINDING SITE FOR RESIDUE NAG C 603
4	AC4	SOFTWARE	ASN A:118 , ASP A:166 , HIS A:167 , TRP A:168	BINDING SITE FOR RESIDUE NAG A 604
5	AC5	SOFTWARE	ARG B:52 , LEU B:54 , ARG B:66 , HOH B:876 , HOH B:893 , HOH B:894 , ARG D:52 , ARG D:66	BINDING SITE FOR RESIDUE SO4 B 800

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 1KTD)

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

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

(no "Exon" information available for 1KTD)

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 d1ktda2 A:1-81 Class II MHC alpha chain, N-terminal domain                       d1ktda1 A:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1ktdA01 A:3-81                                                                 1ktdA02 A:82-181 Immunoglobulins                                                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktd 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:215
 aligned with Q31163_MOUSE | Q31163 from UniProtKB/TrEMBL  Length:263

    Alignment length:215
                                                 28     29                                                                                                                                                                                         
                                    15        25  |     29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
         Q31163_MOUSE     6 VPCVAAVILLLTVLSPPVALVRD------SRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 214
               SCOP domains d1ktdb2 B:1-120 Class II MHC beta chain, N-terminal domain                                                              d1ktdb1 B:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1ktdB01 B:1-118 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1                                  1ktdB02 B:119-215 Immunoglobulins                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................eeeeeeeeeee.hhhh.eeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktd B   1 AADLIAYLKQASAKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
                                    10        20        30        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: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 d1ktdc2 C:1-81 Class II MHC alpha chain, N-terminal domain                       d1ktdc1 C:82-182 Class II MHC alpha chain, C-terminal domain                                          SCOP domains
               CATH domains --1ktdC01 C:3-81                                                                 1ktdC02 C:82-181 Immunoglobulins                                                                    - CATH domains
           Pfam domains (1) ---MHC_II_alpha-1ktdC03 C:4-84                                                      --------C1-set-1ktdC01 C:93-175                                                            ------- Pfam domains (1)
           Pfam domains (2) ---MHC_II_alpha-1ktdC04 C:4-84                                                      --------C1-set-1ktdC02 C:93-175                                                            ------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eee.eeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktd 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:215
 aligned with Q31163_MOUSE | Q31163 from UniProtKB/TrEMBL  Length:263

    Alignment length:215
                                                 28     29                                                                                                                                                                                         
                                    15        25  |     29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
         Q31163_MOUSE     6 VPCVAAVILLLTVLSPPVALVRD------SRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 214
               SCOP domains d1ktdd2 D:1-120 Class II MHC beta chain, N-terminal domain                                                              d1ktdd1 D:121-215 Class II MHC beta chain, C-terminal domain                                    SCOP domains
               CATH domains 1ktdD01 D:1-118 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1                                  1ktdD02 D:119-215 Immunoglobulins                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................eeeeeeeeeee.hhhh.eeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeee........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ktd D   1 AADLIAYLKQASAKGGGGSLVGGGSGGGGSRPWFLEYCKSECHFYNGTQRVRLLVRYFYNLEENLRFDSDVGEFRAVTELGRPDAENWNSQPEFLEQKRAEVDTVCRHNYEIFDNFLVPRRVEPTVTVYPTKTQPLEHHNLLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQSGEVYTCQVEHPSLTDPVTVEW 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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	1ktdA01	A:3-81
1b	1ktdC01	C:3-81
1c	1ktdB01	B:1-118
1d	1ktdD01	D:1-118

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

2a	1ktdA02	A:82-181
2b	1ktdC02	C:82-181
2c	1ktdB02	B:119-215
2d	1ktdD02	D:119-215

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Mus musculus (Mouse) (118)

1a	C1-set-1ktdC01	C:93-175
1b	C1-set-1ktdC02	C:93-175

Clan: MHC (252)

Family: MHC_II_alpha (42)

Mus musculus (Mouse) (16)

2a	MHC_II_alpha-1ktdC03	C:4-84
2b	MHC_II_alpha-1ktdC04	C:4-84

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	:	1iea 1ieb 1kt2
	Q31163_MOUSE \| Q31163	:	3qib 3qiu 3qiw
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1kt2	CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTOCHROME C PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

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 (2, 4)

Gene Ontology (16, 23)

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Related Entries

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Related Entries Specified in the PDB File