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(-) Description

Title :  CRYSTAL STRUCTURE OF SWINE MHC CLASSI FOR 1.48 ANGSTROMS
 
Authors :  S. Fan, N. Zhang, S. Wang, Y. Wu, C. Xia
Date :  25 Dec 15  (Deposition) - 18 May 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Swine; Crystal Structure; Mhc I; Influenza A Virus; Mechanism; Ctl Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fan, Y. Wu, S. Wang, Z. Wang, B. Jiang, Y. Liu, R. Liang, W. Zhou, N. Zhang, C. Xia
Structural And Biochemical Analyses Of Swine Major Histocompatibility Complex Class I Complexes And Prediction Of The Epitope Map Of Important Influenza A Virus Strains
J. Virol. V. 90 6625 2016
PubMed-ID: 27170754  |  Reference-DOI: 10.1128/JVI.00119-16

(-) Compounds

Molecule 1 - MHC CLASS I ANTIGEN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SLA-3*HS0202
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2M
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: LACTOLLIN
 
Molecule 3 - NONAPEPTIDE FROM INFLUENZA A VIRUS HA PROTEIN
    Chains: C, F
    Engineered: YES
    Organism Scientific: H1N1 SWINE INFLUENZA VIRUS
    Organism Taxid: 36420
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5H94)

(-) Sites  (0, 0)

(no "Site" information available for 5H94)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:102 -A:165
2A:204 -A:260
3B:27 -B:81
4D:102 -D:165
5D:204 -D:260
6E:27 -E:81

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:210 -Pro A:211
2His B:33 -Pro B:34
3Tyr D:210 -Pro D:211
4His E:33 -Pro E:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H94)

(-) Exons   (0, 0)

(no "Exon" information available for 5H94)

(-) 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:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeehhhheeeeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee.....eeeeee..ee.hhhhee...ee.....eeeeeeeee...hhh.eeeeee.......eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h94 A   2 GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPREEPRAPWIQQEGQEYWDRETQISKDNAQTYRVNLNNLRGYYNQSEAGSHTFQNMYGCYLGPDGLLLHGYHQYAYDGADYIALNEDLRSWTAADTAAQITKRKWEASGWAEQERSYLQGLCVESLREYLEMGKDTLQRAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD 276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     


Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee.....eeeeee..ee...ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5h94 B   4 ARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 100
                                    13        23        33        43        53        63        73        83        93       


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5h94 C   1 KMNTQFTAV   9


Chain D from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeehhhheeeeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee......eeeeeeeeee.....eeeeee..ee.hhhhee...ee.....eeeeeeeee...hhh.eeeeee.......eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h94 D   2 GPHSLSYFYTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPREEPRAPWIQQEGQEYWDRETQISKDNAQTYRVNLNNLRGYYNQSEAGSHTFQNMYGCYLGPDGLLLHGYHQYAYDGADYIALNEDLRSWTAADTAAQITKRKWEASGWAEQERSYLQGLCVESLREYLEMGKDTLQRAEPPKTHVTRHPSSDLGVTLRCWALGFYPKEISLTWQREGQDQSQDMELVETRPSGDGTFQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD 276
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271     


Chain E from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee.....eeeeee..ee...ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5h94 E   4 ARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDWSFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH 100
                                    13        23        33        43        53        63        73        83        93       


Chain F from PDB  Type:PROTEIN  Length:9
                                         
               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
                 5h94 F   1 KMNTQFTAV   9
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5H94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H94)

(-) Gene Ontology  (22, 22)

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  Cis Peptide Bonds
    His B:33 - Pro B:34   [ RasMol ]  
    His E:33 - Pro E:34   [ RasMol ]  
    Tyr A:210 - Pro A:211   [ RasMol ]  
    Tyr D:210 - Pro D:211   [ RasMol ]  
 
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  5h94
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  A0A0N9JT91_P | A0A0N9JT91
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 Related Entries

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