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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOMEGALOVIRUS GLYCOPROTEIN UL141 TARGETING THE DEATH RECEPTOR TRAIL-R2
 
Authors :  I. Nemcovicova, D. M. Zajonc
Date :  05 Dec 12  (Deposition) - 03 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ig-Like Domain, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Nemcovicova, C. A. Benedict, D. M. Zajonc
Structure Of Human Cytomegalovirus Ul141 Binding To Trail-R Reveals Novel, Non-Canonical Death Receptor Interactions.
Plos Pathog. V. 9 03224 2013
PubMed-ID: 23555243  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1003224

(-) Compounds

Molecule 1 - PROTEIN UL141
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UL141, UNP RESIDUES 32-246
    Organism Common: HHV-5
    Organism Scientific: HUMAN HERPESVIRUS 5
    Organism Taxid: 295027
    Strain: MERLIN
 
Molecule 2 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B
    Chains: C, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: TRAIL-R2, UNP RESIDUES 58-184
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEATH RECEPTOR 5, TNF-RELATED APOPTOSIS-INDUCING LIGAND RECEPTOR 2, TRAIL RECEPTOR 2, TRAIL-R2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric/Biological Unit (4, 26)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NA1Ligand/IonSODIUM ION
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:74 , ASN A:147 , HIS A:150 , NAG A:302 , HOH A:458BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWAREMSE A:42 , HIS A:150 , NAG A:301BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWAREGLN A:62 , TYR A:113 , ASN A:132BINDING SITE FOR RESIDUE NAG A 303
04AC4SOFTWAREHIS A:122 , VAL B:57 , ALA B:58 , THR B:191BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWARETRP B:74 , ASN B:147 , HIS B:150 , NAG B:302 , HOH B:409BINDING SITE FOR RESIDUE NAG B 301
06AC6SOFTWAREHIS B:150 , NAG B:301 , HOH B:411 , HOH B:412 , HOH B:468BINDING SITE FOR RESIDUE NAG B 302
07AC7SOFTWAREARG B:80 , ARG B:82 , MSE B:140 , GLU B:142BINDING SITE FOR RESIDUE CA B 303
08AC8SOFTWARETRP B:116BINDING SITE FOR RESIDUE NA B 304
09AC9SOFTWARELYS D:98 , TYR D:99 , GLY D:100 , ASP D:102 , CYS D:116 , CYS D:129 , THR D:130 , THR D:131BINDING SITE FOR RESIDUE CA D 201
10BC1SOFTWAREASP A:37 , ALA A:39 , HOH A:436 , TYR D:103 , ARG D:115 , THR D:117 , ASN D:134BINDING SITE FOR RESIDUE CA D 202

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:143
2A:84 -A:234
3B:67 -B:143
4B:84 -B:234
5C:81 -C:94
6C:97 -C:113
7C:116 -C:129
8C:119 -C:137
9C:139 -C:153
10C:156 -C:170
11C:160 -C:178
12D:81 -D:94
13D:97 -D:113
14D:116 -D:129
15D:119 -D:137
16D:139 -D:153
17D:156 -D:170
18D:160 -D:178

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser C:149 -Pro C:150
2Ser D:149 -Pro D:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I9X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I9X)

(-) Exons   (0, 0)

(no "Exon" information available for 4I9X)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhh...ee.....eeeeeeeee.....eeeeeeee.......eeeeee.....eeee.........eeeeee...eeeeeeeee......eeeeeeee...eeeeeeeeeee.eeee..................hhh.eeee.eeeee..........hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i9x A  32 PFATADIAEKmWAENYETTSPAPVLVAEGEQVTIPCTVmTHSWPmVSIRARFCRSHDGSDELILDAVKGHRLmNGLQYRLPYATWNFSQLHLGQIFSLTFNVSTDTAGmYECVLRNYSHGLImQRFVILTQLETLSTPALGRYSLGDQIWSPTPWRLRNHRNYFYIGRAPDEEPDRCWTVIQRYRLP 244
                                    41|       51        61        71    |   81        91       101  |    111       121       131       141       151  |    161     ||178       188       198|      227       237       
                                     42-MSE                      70-MSE |                         104-MSE                             140-MSE       154-MSE      167|                    198|     216|                 
                                                                       76-MSE                                                                                     175                     208      227                 


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..hhhhhh...ee.....eeeeeeeee.....eeeeeeee.......eeeeee.....eeee.........eeeeee...eeeeeeeee......eeeeeeee...eeeeeeeeeee..eee................hhhhheee......eeee.......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i9x B  32 PFATADIAEKmWAENYETTSPAPVLVAEGEQVTIPCTVmTHSWPmVSIRARFCRSHDGSDELILDAVKGHRLmNGLQYRLPYATWNFSQLHLGQIFSLTFNVSTDTAGmYECVLRNYSHGLImQRFVILTQLETLPALGRYSLGDQIWSPTPWRLRNHDCGFQRNYFYIGREPDRCWTVIQRYRLPGD 246
                                    41|       51        61        71    |   81        91       101  |    111       121       131       141       151  |    161    || 180       190       200||     214||     238        
                                     42-MSE                      70-MSE |                         104-MSE                             140-MSE       154-MSE     166|                      201|      215|                
                                                                       76-MSE                                                                                    176                       206       230                


Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains d4i9xc1 C:78-114 automated matches   d4i9xc2 C:115-154 automated matches     d4i9xc3 C:155-182            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee......eee.....ee..........ee.......eeeee........eeee...eee.......eee........eee...........eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4i9x C  78 EGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEmCRKCRTGCPRGmVKVGDCTPWSDIECVHKE 182
                                    87        97       107       117       127       137       147    |  157      |167       177     
                                                                                                    152-MSE     164-MSE              


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d4i9xd1 D:75-114 automated matches      d4i9xd2 D:115-154 automated matches     d4i9xd3 D:155-182            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee......eee.....ee..........ee.......eeeee........eeee...eee.......eee........eeeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4i9x D  75 SPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEmCRKCRTGCPRGmVKVGDCTPWSDIECVHKE 182
                                    84        94       104       114       124       134       144       154       164       174        
                                                                                                       152-MSE     164-MSE
   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, 6)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I9X)

(-) Gene Ontology  (36, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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  UL141_HCMVM | Q6RJQ3
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 Related Entries

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

UniProtKB/Swiss-Prot
        TR10B_HUMAN | O14763: 1d0g 1d4v 1du3 1za3 2h9g 3x3f 4n90 4od2
        UL141_HCMVM | Q6RJQ3: 4jm0

(-) Related Entries Specified in the PDB File

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