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(-) Description

Title :  CRYSTAL STRUCTURE OF IAG7 IN COMPLEX WITH RLGL-WE14
 
Authors :  Y. Wang, N. Jin, S. Dai, J. W. Kappler
Date :  08 Sep 15  (Deposition) - 28 Oct 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Chromogranin A, Type I Diabetes, T Cell, Fusion Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Jin, Y. Wang, F. Crawford, J. White, P. Marrack, S. Dai, J. W. Kappler
N-Terminal Additions To The We14 Peptide Of Chromogranin A Create Strong Autoantigen Agonists In Type 1 Diabetes.
Proc. Natl. Acad. Sci. Usa V. 112 13318 2015
PubMed-ID: 26453556  |  Reference-DOI: 10.1073/PNAS.1517862112

(-) Compounds

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-D ALPHA CHAIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Taxid: 7111
    Gene: I-AG7
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: NOD
 
Molecule 2 - BETA CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II, I- AG7,H2-AB1 PROTEIN
    Chains: B, D, F, H
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 31-215
    Gene: H2-AB1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: MHC CLASS II H2-IA-BETA CHAIN (HAPLOTYPE NOD)

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:-20 , TRP B:-22 , ARG B:71 , HOH B:401 , ARG H:-20 , TRP H:-22 , ARG H:71 , HOH H:308binding site for residue FLC B 301
2AC2SOFTWARETRP D:-22 , ARG D:-20 , ARG D:71 , ARG F:-20 , TRP F:-22 , ARG F:71 , HOH F:404binding site for residue FLC F 301
3AC3SOFTWAREILE H:104 , LEU H:106 , LEU H:118 , TYR H:174 , GLU H:190binding site for Di-peptide TRP H 191 and ARG H 192
4AC4SOFTWAREILE H:104 , LEU H:106 , LEU H:118 , TYR H:174 , GLU H:190binding site for Di-peptide TRP H 191 and ARG H 192

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:109 -A:165
2B:16 -B:80
3B:120 -B:176
4C:109 -C:165
5D:16 -D:80
6D:120 -D:176
7E:109 -E:165
8F:16 -F:80
9F:120 -F:176
10G:109 -G:165
11H:16 -H:80
12H:120 -H:176

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Ser A:17 -Pro A:18
2Phe A:115 -Pro A:116
3Tyr B:126 -Pro B:127
4Ser C:17 -Pro C:18
5Phe C:115 -Pro C:116
6Tyr D:126 -Pro D:127
7Gln D:139 -Glu D:140
8Ser E:17 -Pro E:18
9Phe E:115 -Pro E:116
10Tyr F:126 -Pro F:127
11Ser G:17 -Pro G:18
12Phe G:115 -Pro G:116
13Tyr H:126 -Pro H:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DMK)

(-) Sequences/Alignments

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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee............hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk A   2 IEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGL 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeeee.eeeeeeeeee.....eeeeee..ee....eeee..ee.....eeeeeeeee.......eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk B -27 SRLGLWSRMDQLERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWR 192
                                   -18 ||     12        22        32        42        52        62  |||   74        84        94 ||    105 ||    122       132       142       152       162       172       182       192
                                     -16|                                                          65||                         96|      107|                                                                             
                                        5                                                           67|                          98       115                                                                             
                                                                                                     69                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee............hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.........eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk C   1 DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLE 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain D from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeeee..eeeeeeeee.....eeeee......eee...ee.....eeeeeee.........eeeee.......eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dmk D -27 SRLGLWSRMDQLERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSHNTLVCSVTDFYPAKIKVRWFQEETVGVSSTQLIRNGDWTFQVLVMLEMPHQGEVYTCHVEHPSLKSPITVEWR 192
                                   -18 ||     12        22        32        42        52        62  |||   74        84        94 ||    105 ||    122       132  ||   145       155       165||     176       186      
                                     -16|                                                          65||                         96|      107|                 135|                        166|                        
                                        5                                                           67|                          98       115                  139                         168                        
                                                                                                     69                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee...eeeeeeee..eeeeee......eee............hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee........eee...ee.....eeeeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk E   1 DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLE 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain F from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeeee.eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk F -27 SRLGLWSRMDQLERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWR 192
                                   -18 ||     12        22        32        42        52        62  |||   74        84        94 ||    105 ||    122       132       142       152       162       172       182       192
                                     -16|                                                          65||                         96|      107|                                                                             
                                        5                                                           67|                          98       115                                                                             
                                                                                                     69                                                                                                                   


Chain G from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk G   1 DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLE 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain H from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....eeeeee..eeeeeeeeee.....eeeeee..ee....eeee..ee.....eeeeeeeee.......eeeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dmk H -27 SRLGLWSRMDQLERHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEW 191
                                   -18 ||     12        22        32        42        52        62  |||   74        84        94 ||    105 ||    122       132       142       152       162       172       182         
                                     -16|                                                          65||                         96|      107|                                                                            
                                        5                                                           67|                          98       115                                                                            
                                                                                                     69
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DMK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 22)

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  5dmk
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  Q31135_MOUSE | Q31135
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HA2D_MOUSE | P04228: 1es0 1f3j 1iao 2iad 3cup 3mbe
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