4H26 - JenaLib

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Title :   TCR INTERACTION WITH PEPTIDE MIMICS OF NICKEL OFFERS STRUCTURE INSIGHT TO NICKEL CONTACT ALLERGY

Authors :   J. W. Kappler, L. Yin, S. Dai, P. Marrack, F. Crawford

Date :   12 Sep 12 (Deposition) - 16 Oct 13 (Release) - 16 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Protein-Protein Complex, Immunoglobulin Fold, Antigen Presentation, Tcr, Cell Surface, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Yin, F. Crawford, P. Marrack, J. W. Kappler, S. Dai
T-Cell Receptor (Tcr) Interaction With Peptides That Mimic Nickel Offers Insight Into Nickel Contact Allergy.
Proc. Natl. Acad. Sci. Usa V. 109 18517 2012
PubMed-ID: 23091041 | Reference-DOI: 10.1073/PNAS.1215928109

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Gene	:	HLA-DRA, HLA-DRA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS II ANTIGEN DRA

Molecule 2 - MHC CLASS II ANTIGEN
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Taxid	:	9606
	Gene	:	HLA-DRB3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MHC CLASS II ANTIGEN DRB3

Molecule 3 - PEPTIDE
	Chains	:	C, F
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

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

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:117 , ASN A:118 , GLU A:166 , TRP A:168 , ASN E:19 , THR E:21 , GLU E:22	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 118 RESIDUES 601 TO 602
2	AC2	SOFTWARE	GLU B:22 , ASN D:118 , GLU D:166 , TRP D:168	BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 118 RESIDUES 201 TO 202
3	AC3	SOFTWARE	GLN A:9 , TRP A:43 , ALA A:52 , SER A:53 , PHE A:54 , GLU A:55 , ASN A:62 , VAL A:65 , ASN A:69 , ILE A:72 , MET A:73 , HOH A:718 , LEU B:11 , SER B:13 , PHE B:26 , GLU B:28 , TYR B:30 , PHE B:37 , VAL B:50 , VAL B:57 , TRP B:61 , GLN B:64 , LEU B:67 , LYS B:71 , GLN B:74 , THR B:77 , TYR B:78 , HIS B:81 , ASN B:82 , VAL B:85 , HOH C:401 , HOH C:402 , HOH C:405 , HOH C:406 , GLU D:172	BINDING SITE FOR CHAIN C OF PEPTIDE
4	AC4	SOFTWARE	GLU A:172 , HOH A:717 , GLN D:9 , ALA D:52 , SER D:53 , PHE D:54 , ASN D:62 , VAL D:65 , ASN D:69 , ILE D:72 , MET D:73 , LEU E:11 , SER E:13 , PHE E:26 , GLU E:28 , TYR E:30 , TRP E:61 , GLN E:64 , LYS E:71 , GLN E:74 , THR E:77 , TYR E:78 , HIS E:81 , ASN E:82 , VAL E:85 , HOH F:401 , HOH F:402 , HOH F:403 , HOH F:404 , HOH F:405	BINDING SITE FOR CHAIN F OF PEPTIDE

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Asn A:15	-	Pro A:16
2	Thr A:113	-	Pro A:114
3	Tyr B:123	-	Pro B:124
4	Asn D:15	-	Pro D:16
5	Thr D:113	-	Pro D:114
6	Tyr E:123	-	Pro E:124

(no "SAP(SNP)/Variant" information available for 4H26)

(no "PROSITE Motif" information available for 4H26)

(no "Exon" information available for 4H26)

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:179
                                                                                                                                                                                                                   
               SCOP domains d4h26a1 A:3-81 Class II MHC alpha chain, N-terminal domain                     d4h26a2 A:82-181 Class II MHC alpha chain, C-terminal domain                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhh...........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee..........eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h26 A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains d4h26b1 B:3-92 automated matches                                                          d4h26b2 B:93-190 automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h26 B   3 TRPRFLELLKSECHFFNGTERVRFLERYFHNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGQVDTYCRHNYGVVESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4h26 C 306 QWIRVNIPKRI 316
                                   315

Chain D from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains d4h26d1 D:3-81 Class II MHC alpha chain, N-terminal domain                     d4h26d2 D:82-181 Class II MHC alpha chain, C-terminal domain                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h26 D   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain E from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains d4h26e1 E:3-92 automated matches                                                          d4h26e2 E:93-190 automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee....eeeeeeeeee...eeeeee.....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h26 E   3 TRPRFLELLKSECHFFNGTERVRFLERYFHNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGQVDTYCRHNYGVVESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain F from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4h26 F 306 QWIRVNIPKRI 316
                                   315

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 '\|'

(no "CATH Domain" information available for 4H26)

(no "Pfam Domain" information available for 4H26)

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	Cis Peptide Bonds
		Asn A:15 - Pro A:16	[ RasMol ]
		Asn D:15 - Pro D:16	[ RasMol ]
		Thr A:113 - Pro A:114	[ RasMol ]
		Thr D:113 - Pro D:114	[ RasMol ]
		Tyr B:123 - Pro B:124	[ RasMol ]
		Tyr E:123 - Pro E:124	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (6, 6)

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