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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE CYTOMEGALOVIRUS MHC-I HOMOLOG M152 WITH LIGAND RAE-1 GAMMA
 
Authors :  R. Wang, K. Natarajan, D. H. Margulies
Date :  17 Jul 12  (Deposition) - 19 Dec 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Mhc-I Fold, Immunoevasion, Stress Induced Ligand, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wang, K. Natarajan, M. J. Revilleza, L. F. Boyd, L. Zhi, H. Zhao, H. Robinson, D. H. Margulies
Structural Basis Of Mouse Cytomegalovirus M152/Gp40 Interaction With Rae1Gamma Reveals A Paradigm For Mhc/Mhc Interaction In Immune Evasion.
Proc. Natl. Acad. Sci. Usa V. 109 E3578 2012
PubMed-ID: 23169621  |  Reference-DOI: 10.1073/PNAS.1214088109

(-) Compounds

Molecule 1 - RETINOIC ACID EARLY-INDUCIBLE PROTEIN 1-GAMMA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RAET1C
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: RAE-1-GAMMA
 
Molecule 2 - M152 PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: DROSOPHILA
    Expression System Taxid: 7215
    Gene: M152
    Organism Common: MUHV-1
    Organism Scientific: MURID HERPESVIRUS 1
    Organism Taxid: 10366

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:61 , SER C:63BINDING SITE FOR RESIDUE NAG C 401
2AC2SOFTWAREASN C:208BINDING SITE FOR RESIDUE NAG C 402
3AC3SOFTWAREASN D:208 , SER D:210BINDING SITE FOR RESIDUE NAG D 401
4AC4SOFTWAREASN D:61 , SER D:63BINDING SITE FOR RESIDUE NAG D 402

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:7 -A:26
2A:60 -A:160
3B:7 -B:26
4B:60 -B:160
5C:16 -C:170
6C:99 -C:106
7D:16 -D:170
8D:99 -D:106

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Tyr A:98 -Pro A:99
2Val C:102 -Pro C:103
3His B:84 -Lys B:85
4Tyr B:98 -Pro B:99
5Val D:102 -Pro D:103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G59)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G59)

(-) Exons   (0, 0)

(no "Exon" information available for 4G59)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains d4g59a_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee..........eeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeee..........eeeeee...eeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g59 A   2 AHSLRCNLTIKAPTPADPLWYEAKCLVDEILILHLSNINKANATEVGECLTQPVNDLCQKLRDKVSNTKVDTHKTNGYPHLQVTMIYPQSQGQTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWNDDGDLVQRLKYFIPECRQKIDEFLKQSKE 173
                                    11        21        31        41|       61        71        81        91       101       111       121       131       141       151       161       171  
                                                                  41|                                                                                                                         
                                                                   52                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains d4g59b_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..........eeeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee..........eeeeee...eeeeee....eeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g59 B   2 AHSLRCNLTIKAPTPADPLWYEAKCLVDEILILHLSNINKTANATEVGECLTQPVNDLCQKLRDKVSNTKVDTHKTNGYPHLQVTMIYPQSQGQTPSATWEFNISDSYFFTFYTENMSWRSANDESGVIMNKWNDDGDLVQRLKYFIPECRQKIDEFLKQSKE 173
                                    11        21        31        41||      60        70        80        90       100       110       120       130       140       150       160       170   
                                                                   42|                                                                                                                         
                                                                    52                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..........eeeeeeeeee..eeeeeee.......eee.....ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..eeeeeee....eee..........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee....eeeeeeee......eeee......eeeeee.....eeeeeeee...........eeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g59 C   1 SYMDVRIFEDERVDICQDLTATFISYREGPEMFRHSINLEQSSDIFRIEASGEVKHFPWMNVSELAQESAFFVEQERFVYEYIMNVFKAGRPVVFEYRCKFVPFECTVLQMMDGNTLTRYTVDKGVETLGSPPYSPDVSEDDIARYGQGSGISILRDNAALLQKRWTSFCRKIVAMDNPRHNEYSLYSNRGNGYVSCTMRTQVPLAYNISLANGVDIYKYMRMYSGGRLKVEAWLDLRDLNGSTDFAFVISSPTGWYATVKYSE 264
                                    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    


Chain D from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..........eeeeeeeeee..eeeeeeee....eeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..eeeeee.....eee..........hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee......eeee......eeeeee.....eeeeeeee.hhhh......eeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g59 D   1 SYMDVRIFEDERVDICQDLTATFISYREGPEMFRHSINLEQSSDIFRIEASGEVKHFPWMNVSELAQESAFFVEQERFVYEYIMNVFKAGRPVVFEYRCKFVPFECTVLQMMDGNTLTRYTVDKGVETLGSPPYSPDVSEDDIARYGQGSGISILRDNAALLQKRWTSFCRKIVAMDNPRHNEYSLYSNRGNGYVSCTMRTQVPLAYNISLANGVDIYKYMRMYSGGRLKVEAWLDLRDLNGSTDFAFVISSPTGWYATVKYSE 264
                                    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
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G59)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G59)

(-) Gene Ontology  (17, 18)

Asymmetric Unit(hide GO term definitions)

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