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(-) Description

Title :  STRUCTURE OF TOBACCO STREAK VIRUS COAT PROTEIN DIMER AT 2.4 ANGSTROMS RESOLUTION
 
Authors :  A. Gulati, M. R. N. Murthy
Date :  13 Feb 15  (Deposition) - 20 Jan 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Domain-Swapped Dimer, Jelly Roll Beta-Barrel, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Gulati, K. Alapati, A. Murthy, H. S. Savithri, M. R. N. Murthy
Structural Studies On Tobacco Streak Virus Coat Protein: Insights Into The Pleomorphic Nature Of Ilarviruses
J. Struct. Biol. V. 193 95 2016
PubMed-ID: 26706030  |  Reference-DOI: 10.1016/J.JSB.2015.12.007

(-) Compounds

Molecule 1 - COAT PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 73-238
    Organism Scientific: TOBACCO STREAK VIRUS
    Organism Taxid: 12317

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A    F
Biological Unit 2 (1x):  BC   
Biological Unit 3 (1x):    DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CME6Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:173 , LYS A:174 , THR A:177 , ARG A:179 , HOH A:483 , HOH A:498 , ASN F:236binding site for residue EDO A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y6T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y6T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y6T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y6T)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y6T)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.............eeeehhhhhh.........eeeeeeeeeee...eeeeee............eee.....eeeeeeeeeee.hhh...eeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6t A  89 TSLKLPNNQVWVTRKASEWSAKTIDTNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGVIPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                    98       108       118       128       138       148       162       172       182       192       202       212       222       232      
                                                                                              157|                                    201-CME                                 
                                                                                               162                                                                            


Chain B from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee............eeeehhhhhh.........eeeeeeeeeee...eeeeeee...........eee.....eeeeeeeeeee.hhh..eeeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y6t B  90 SLKLPNNQVWVTRKASEWSAKTITNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGVIPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                    99       109  ||   120       130       140       150     ||164       174       184       194      |204       214       224       234    
                                                112|                                       156|                                     201-CME                                 
                                                 114                                        161                                                                             


Chain C from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.............eeeehhhhhh.........eeeeeeeeeee...eeeeee..............eee.....eeeeeeeeeee.hhh...eeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6t C  91 LKLPNNQVWVTRKASEWSAKTIDTNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGVTVIPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                   100       110       120       130       140       150       162       172       182       192       202       212       222       232      
                                                                                             158|                                     201-CME                                 
                                                                                              161                                                                             


Chain D from PDB  Type:PROTEIN  Length:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee..........eeeehhhhhh.........eeeeeeeeeee...eeeeee...............eee.....eeeeeeeeeee.hhh...eeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y6t D  91 LKLPNNQVWVTRKASEWSAKTNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGVGDVIPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                   100       110|      123       133       143       153   ||  164       174       184       194      |204       214       224       234    
                                             110|                                        157|                                       201-CME                                 
                                              114                                         159                                                                               


Chain E from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.............eeeehhhhhh.........eeeeeeeeeee...eeeeee...............eee.....eeeeeeeeeee.hhh...eeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6t E  90 SLKLPNNQVWVTRKASEWSAKTIDTNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGVTDVIPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                    99       109       119       129       139       149       160       170       180       190       200|      210       220       230        
                                                                                              158|                                      201-CME                                 
                                                                                               160                                                                              


Chain F from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..........eeeehhhhhh.........eeeeeeeeeee...eeeeeee.........eee.....eeeeeeeeeee.hhh..eeeeeee.........eee..eeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6t F  90 SLKLPNNQVWVTRKASEWSAKTNDAIPFKTIVEGIPEINSETKFYRLLIGFVAVSDGTFGMVDGPDPPVVGRLGFKKNTYRSRDFDLGGKLLNQLDDRAIVWcLDERRRDAKRVQLAGYWIAISKPAPLMPPEDFLVNQD 238
                                    99       109 ||    122       132       142       152   ||  168       178       188       198  |    208       218       228       238
                                               111|                                      156|                                   201-CME                                 
                                                115                                       163
   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 4Y6T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y6T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y6T)

(-) Gene Ontology  (4, 4)

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(-) Related Entries Specified in the PDB File

4y6x