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(-) Description

Title :  CRYSTAL STRUCTURE OF THE H2DB IN COMPLEX WITH THE NP-N5H PEPTIDE
 
Authors :  J. Rossjohn, S. Gras
Date :  16 Jun 13  (Deposition) - 16 Oct 13  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Influenza, Viral Escape, T Cell Immunity, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Valkenburg, S. Quinones-Parra, S. Gras, N. Komadina, J. Mcvernon, Z. Wang, H. Halim, P. Iannello, C. Cole, K. Laurie, A. Kelso, J. Rossjohn, P. C. Doherty, S. J. Turner, K. Kedzierska
Acute Emergence And Reversion Of Influenza A Virus Quasispecies Within Cd8(+) T Cell Antigenic Peptides.
Nat Commun V. 4 2663 2013
PubMed-ID: 24173108  |  Reference-DOI: 10.1038/NCOMMS3663

(-) Compounds

Molecule 1 - H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 25-304
    Gene: H2-D1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: HEAVY CHAIN H2DB, H-2D(B)
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 21-119
    Gene: B2M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: B2M
 
Molecule 3 - NP-N5H PEPTIDE
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:194BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREPRO A:20 , ARG A:75 , ARG A:79 , PEG A:303BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARESER A:13 , PRO A:20 , ARG A:75 , ARG A:79 , LEU A:82 , HIS A:93 , SO4 A:302 , HOH A:408BINDING SITE FOR RESIDUE PEG A 303
4AC4SOFTWARELYS B:58BINDING SITE FOR RESIDUE NA B 101

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:164
2A:203 -A:259
3B:25 -B:80

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:209 -Pro A:210
2His B:31 -Pro B:32
3Pro B:72 -Thr B:73
4Glu B:74 -Thr B:75
5Thr B:75 -Asp B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L8B)

(-) Exons   (0, 0)

(no "Exon" information available for 4L8B)

(-) Sequences/Alignments

Asymmetric/Biological 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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4l8ba1 A:1-181 Class I MHC, alpha-1 and alpha-2 domains                                                                                                                             d4l8ba2 A:182-276 Class I MHC, alpha-3 domain                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee.........ee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l8b A   1 GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYWERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEGRDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLLRTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      


Chain B from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains d4l8bb_ B: beta2-microglobulin                                                                     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
                 4l8b B   2 QKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM  99
                                    11        21        31        41        51        61        71        81        91        


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
                 4l8b C   1 ASNEHMETM   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L8B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L8B)

(-) Gene Ontology  (57, 71)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:74 - Thr B:75   [ RasMol ]  
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    Thr B:75 - Asp B:76   [ RasMol ]  
    Tyr A:209 - Pro A:210   [ RasMol ]  
 

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  HA11_MOUSE | P01899
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_MOUSE | P01887: 1bii 1bqh 1bz9 1cd1 1ddh 1ffn 1ffo 1ffp 1fg2 1fo0 1fzj 1fzk 1fzm 1fzo 1g6r 1g7p 1g7q 1hoc 1inq 1jpf 1jpg 1juf 1k8d 1kbg 1kj2 1kj3 1kpu 1kpv 1l6q 1ld9 1ldp 1leg 1lek 1lk2 1mhc 1mwa 1n3n 1n59 1n5a 1nam 1nan 1nez 1osz 1p1z 1p4l 1pqz 1qo3 1rjy 1rjz 1rk0 1rk1 1s7q 1s7r 1s7s 1s7t 1s7u 1s7v 1s7w 1s7x 1t0m 1t0n 1u58 1vac 1vad 1wbx 1wby 1wbz 1yn6 1yn7 1z5l 1zhb 1zhn 1zt1 1zt7 2akr 2ckb 2clv 2clz 2fik 2fo4 2fwo 2gaz 2mha 2ol3 2q7y 2qri 2qrs 2qrt 2vaa 2vab 2ve6 2zok 2zol 2zsv 2zsw 3arb 3ard 3are 3arf 3arg 3au1 3buy 3c8k 3cc5 3cch 3ch1 3cpl 3cvh 3dmm 3e6f 3e6h 3ecb 3fol 3fom 3fon 3ftg 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3l3h 3ma7 3nwm 3o8x 3o9w 3p4m 3p4n 3p4o 3p9l 3p9m 3pab 3pqy 3pwu 3qi9 3quk 3qul 3qux 3quy 3quz 3rgv 3rol 3roo 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3ta3 3tbs 3tbt 3tbv 3tbw 3tby 3tn0 3to4 3tvm 3ubx 3vj6 3ws3 3ws6 4apq 4ei5 4elm 4hs3 4huu 4huv 4huw 4hux 4hv8 4iho 4irj 4irs 4l8c 4l8d 4mng 4mq7 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zus 4zut 4zuu 4zuv 4zuw 5e8n 5e8o 5e8p 5efi 5fkp 5ivx 5j6g 5j6h 5jwd 5jwe 5sws 5swz
        HA11_MOUSE | P01899: 1bz9 1ce6 1ffn 1ffo 1ffp 1fg2 1hoc 1inq 1jpf 1jpg 1juf 1n3n 1n5a 1qlf 1s7u 1s7v 1s7w 1s7x 1wbx 1wby 1yn6 1yn7 1zhb 2cii 2f74 2ve6 2zok 2zol 3buy 3cc5 3cch 3ch1 3cpl 3ftg 3l3h 3pqy 3quk 3qul 3tbs 3tbt 3tbv 3tbw 3tby 3ws3 3ws6 4huu 4huv 4huw 4hux 4hv8 4iho 4l8c 4l8d 4nsk 4pg2 5e8n 5e8o 5e8p 5jwd 5jwe 5sws 5swz

(-) Related Entries Specified in the PDB File

4huu 4huv 4huw 4hux 4hv8 4l8c 4l8d