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(-) Description

Title :  STRUCTURE OF AVIAN REOVIRUS SIGMA C 117-326, C2 CRYSTAL FORM
 
Authors :  P. Guardado-Calvo, G. C. Fox, A. L. Llamas-Saiz, J. Benavente, M. J. Van Raaij
Date :  14 Apr 08  (Deposition) - 13 Jan 09  (Release) - 15 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha-Helical Coiled Coil, Receptor-Binding, Triple Beta-Spiral, Viral Protein, Virion, Coiled Coil, Beta-Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Guardado-Calvo, G. C. Fox, A. L. Llamas-Saiz, M. J. Van Raaij
Crystallographic Structure Of The Alpha-Helical Triple Coiled-Coil Domain Of Avian Reovirus S1133 Fibre.
J. Gen. Virol. V. 90 672 2009
PubMed-ID: 19218213  |  Reference-DOI: 10.1099/VIR.0.008276-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGMA-C CAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C-PLUS
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Variant: DE3
    Fragment: RESIDUES 117-326
    Organism Scientific: AVIAN REOVIRUS
    Organism Taxid: 38170
    Other Details: THE AVIAN REOVIRUS STRAIN S1133 WAS ORIGINALLY PROVIDED BY DR. PHILIP I.MARCUS WHEN DR. J.BENAVENTE WAS A ROCHE VISITING SCIENTIST IN THE LABORATORY OF DR. A.SHATKIN
    Strain: S1133
    Synonym: SIGMA-3 PROTEIN, SIGMA C

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4ZN7Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:138 , ASN B:138 , ASN C:138BINDING SITE FOR RESIDUE CL C 1327
02AC2SOFTWAREASN A:124 , ASN B:124 , ASN C:124BINDING SITE FOR RESIDUE CL C 1328
03AC3SOFTWARELYS B:150 , ALA B:261 , ARG B:299 , HOH B:2302 , HOH B:2303 , HOH B:2304BINDING SITE FOR RESIDUE GOL B 1327
04AC4SOFTWARELEU A:260 , ALA A:261 , VAL A:264 , ARG A:299 , HOH A:2319 , HOH A:2348 , HOH A:2349BINDING SITE FOR RESIDUE GOL A 1327
05AC5SOFTWARETHR B:143 , ASP B:147 , LEU B:250 , SER B:251 , LEU B:260 , ARG B:299 , HOH B:2227BINDING SITE FOR RESIDUE GOL B 1328
06AC6SOFTWAREHIS A:158 , HOH A:2350 , HIS B:158 , HIS C:158BINDING SITE FOR RESIDUE ZN A 1328
07AC7SOFTWAREASP A:144 , HOH A:2351 , HIS B:255 , HIS C:255BINDING SITE FOR RESIDUE ZN A 1329
08AC8SOFTWAREASP A:134 , ARG B:201 , ASP B:215BINDING SITE FOR RESIDUE ZN A 1330
09AC9SOFTWAREHIS A:287 , TYR A:289 , HOH A:2352 , ASP C:122BINDING SITE FOR RESIDUE ZN A 1331
10BC1SOFTWAREASP B:122 , HIS C:287 , TYR C:289BINDING SITE FOR RESIDUE ZN C 1329
11BC2SOFTWAREASP A:122 , HIS B:287 , TYR B:289 , HOH B:2306BINDING SITE FOR RESIDUE ZN B 1329
12BC3SOFTWAREASP A:212 , THR A:213BINDING SITE FOR RESIDUE ZN A 1332
13BC4SOFTWARESER A:137 , LEU A:140 , GLN B:199 , PHE B:200 , ARG B:201 , HIS B:255 , HOH B:2148BINDING SITE FOR RESIDUE SO4 B 1330

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VRS)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:164 -Pro A:165
2Pro B:164 -Pro B:165
3Pro C:164 -Pro C:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VRS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VRS)

(-) Exons   (0, 0)

(no "Exon" information available for 2VRS)

(-) 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:205
 aligned with SIGC_ARVS1 | Q992I2 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:205
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     
           SIGC_ARVS1   122 DGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...eeee..eeee......eee...eee.....eeeeeeeeeeeee....eeeeeeeeeee..eeeeeeeee.eeee...eeeeeee.........hhhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee..eeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrs A 122 DGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with SIGC_ARVS1 | Q992I2 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:205
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     
           SIGC_ARVS1   122 DGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee...eeee..eeee......eee...eee.....eeeeeeeeeeeee....eeeeeeeeeee..eeeeeee..........eeeeeee.hhh.....hhhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee..eeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vrs B 122 DGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     


Chain C from PDB  Type:PROTEIN  Length:210
 aligned with SIGC_ARVS1 | Q992I2 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:210
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
           SIGC_ARVS1   117 LQTTVDGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Reo_sigmaC-2vrsC01 C:117-326                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) Reo_sigmaC-2vrsC02 C:117-326                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) Reo_sigmaC-2vrsC03 C:117-326                                                                                                                                                                                       Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee...eeee..eeee.......ee...ee......eeeeeeeeeeee.....eeeeeeeeeee..eeeeeeeee........eeeeeee.........hhhhhh.hhhhhh..eeeeeeeee..eeeeeeeeeeeee..eeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vrs C 117 LQTTVDGNSTAISNLKSDISSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYFCSQRVSLTSYSAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTSNVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVFTITFPTGGDGTANIRSLTVRTGIDT 326
                                   126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
   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 2VRS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VRS)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Reo_sigma (16)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SIGC_ARVS1 | Q992I2)
biological process
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  2vrs
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  SIGC_ARVS1 | Q992I2
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 Related Entries

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

UniProtKB/Swiss-Prot
        SIGC_ARVS1 | Q992I2: 2bsf 2bt7 2bt8 2jjl

(-) Related Entries Specified in the PDB File

2bsf STRUCTURE OF THE C-TERMINAL RECEPTOR-BINDING DOMAIN OF AVIAN REOVIRUS FIBRE SIGMAC, ZN CRYSTAL FORM.
2jjl STRUCTURE OF AVIAN REOVIRUS SIGMA C 117-326, P321 CRYSTAL FORM