5KSU - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HLA-DQ2.5-CLIP1 AT 2.73 RESOLUTION

Authors :   T. -B. Nguyen, P. Jayaraman, E. Bergseng, M. S. Madhusudhan, C. -Y. Kim, L. M. Sollid

Date :   10 Jul 16 (Deposition) - 05 Apr 17 (Release) - 05 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.73

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

Keywords :   Hla, Mhc, Dq2. 5, Clip, Celiac Disease, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. B. Nguyen, P. Jayaraman, E. Bergseng, M. S. Madhusudhan, C. -Y. Kim, L. M. Sollid
Structural Basis For The Class-Ii-Associated Invariant Chai Peptide-Rich Phenotype Of Human Leukocyte Antigen Dq2. 5
J. Biol. Chem. 2017
PubMed: search | Reference-DOI: 10.1074/JBC.M117.785139

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ ALPHA 1 CHAIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Taxid	:	10469
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 1-193
	Gene	:	HLA-DQA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DC-1 ALPHA CHAIN,DC-ALPHA,HLA-DCA,MHC CLASS II DQA1

Molecule 2 - MHC CLASS II HLA-DQ-BETA-1
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Taxid	:	10469
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 1-198
	Gene	:	HLA-DQB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN
	Chains	:	C, F
	Engineered	:	YES
	Expression System	:	UNIDENTIFIED BACULOVIRUS
	Expression System Taxid	:	10469
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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)

(no "Ligand,Modified Residues,Ions" information available for 5KSU)

(no "Site" information available for 5KSU)

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	Gly A:17	-	Pro A:18
2	Phe A:113	-	Pro A:114
3	Tyr B:123	-	Pro B:124
4	Gly D:17	-	Pro D:18
5	Phe D:113	-	Pro D:114
6	Tyr E:123	-	Pro E:124

(no "SAP(SNP)/Variant" information available for 5KSU)

(no "PROSITE Motif" information available for 5KSU)

(no "Exon" information available for 5KSU)

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
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeee..eeeeeeehhhheeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksu A   0 DIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPE 181
                                     9|       18        28        38        48   ||   59        69        79        89        99       109       119       129       139       149       159       169       179  
                                     9A                                         52|                                                                                                                               
                                                                                 54

Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ksu B   3 SPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 190
                                    12        22        32        42        52        62        72        82        92       102 ||    120       130       140       150       160       170       180       190
                                                                                                                               104|                                                                             
                                                                                                                                113

Chain C from PDB  Type:PROTEIN  Length:14
                                              
               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
                 5ksu C  -4 PVSKMRMATPLLMQ  10
                               ||    6    
                              -1|         
                                1

Chain D from PDB  Type:PROTEIN  Length:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeee..eeeeeee....eeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksu D   0 DIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPE 181
                                     9|       18        28        38        48   ||   59        69        79        89        99       109       119       129       139       149       159       169       179  
                                     9A                                         52|                                                                                                                               
                                                                                 54

Chain E from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee........eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksu E   3 SPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWR 189
                                    12        22        32        42        52        62        72        82        92       102 ||    120       130       140       150       160       170       180         
                                                                                                                               104|                                                                            
                                                                                                                                113

Chain F from PDB  Type:PROTEIN  Length:14
                                              
               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
                 5ksu F  -4 PVSKMRMATPLLMQ  10
                               ||    6    
                              -1|         
                                1

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 "SCOP Domain" information available for 5KSU)

(no "CATH Domain" information available for 5KSU)

(no "Pfam Domain" information available for 5KSU)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5ksu)

	Sites
(no "Sites" information available for 5ksu)

	Cis Peptide Bonds
		Gly A:17 - Pro A:18	[ RasMol ]
		Gly D:17 - Pro D:18	[ RasMol ]
		Phe A:113 - Pro A:114	[ RasMol ]
		Phe D:113 - Pro D:114	[ RasMol ]
		Tyr B:123 - Pro B:124	[ RasMol ]
		Tyr E:123 - Pro E:124	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	5ksu
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	HG2A_HUMAN \| P04233
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	O19712_HUMAN \| O19712
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	Q5Y7D3_HUMAN \| Q5Y7D3
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UniProtKB/Swiss-Prot
	DQA1_HUMAN \| P01909	:	1jk8 1nbn 1s9v 1uvq 2nna 4gg6 4ozf 4ozg 4ozh 4ozi 5ksa 5ksb 5ksv
	HG2A_HUMAN \| P04233	:	1a6a 1icf 1iie 1l3h 1muj 3pdo 3pgc 3pgd 3qxa 3qxd 4aen 4ah2 4x5w 5ksv
	O19712_HUMAN \| O19712	:	5ksv
	Q5Y7D3_HUMAN \| Q5Y7D3	:	4d8p
UniProtKB/TrEMBL
	Q5Y7D3_HUMAN \| Q5Y7D3	:	4ozf 4ozg 4ozh 4ozi 5ksv

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (85, 120)

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