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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STEM AND RECEPTOR BINDING DOMAIN OF THE SPIKE PROTEIN P1 FROM BACTERIOPHAGE PM2
 
Authors :  N. G. A. Abrescia, J. M. Grimes, H. K. Kivela, R. Assenberg, G. C. Sutton, S. J. Butcher, J. K. H. Bamford, D. H. Bamford, D. I. Stuart
Date :  06 Jun 08  (Deposition) - 16 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Viral Stem-Receptor Binding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. A. Abrescia, J. M. Grimes, H. K. Kivela, R. Assenberg, G. C. Sutton, S. J. Butcher, J. K. H. Bamford, D. H. Bamford, D. I. Stuart
Insights Into Virus Evolution And Membrane Biogenesis From The Structure Of The Marine Lipid- Containing Bacteriophage Pm2.
Mol. Cell V. 31 749 2008
PubMed-ID: 18775333  |  Reference-DOI: 10.1016/J.MOLCEL.2008.06.026

(-) Compounds

Molecule 1 - SPIKE PROTEIN P1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINF
    Expression System Strain: B834
    Expression System Taxid: 562
    Fragment: STEM-RECEPTOR BINDING DOMAIN, RESIDUES 82-335
    Organism Common: BACTERIOPHAGE PM2
    Organism Scientific: PSEUDOALTEROMONAS PHAGE PM2
    Organism Taxid: 10661
    Other Details: CLONED FRAGMENT STARTS AT RESIDUE 82 AND STOPS AT RESIDUE 335
    Synonym: P1-RECEPTOR BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:231 , ASP B:293 , ASP B:295 , HOH B:2153 , HOH B:2202 , HOH B:2205BINDING SITE FOR RESIDUE CA B1336
2AC2SOFTWARESER A:231 , ASP A:293 , ASP A:295 , HOH A:2207 , HOH A:2254 , HOH A:2256BINDING SITE FOR RESIDUE CA A1336
3AC3SOFTWAREGLN B:301 , ASP B:303 , HOH B:2210 , HOH B:2212 , HOH B:2223BINDING SITE FOR RESIDUE CA B1337
4AC4SOFTWAREGLN B:301 , ASP B:303 , ASP B:306 , HOH B:2011 , HOH B:2209 , HOH B:2210BINDING SITE FOR RESIDUE CA B1338
5AC5SOFTWAREARG A:105 , LYS A:179 , ASN A:193BINDING SITE FOR RESIDUE CL A1337

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VVE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VVE)

(-) 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:252
 aligned with SPIKE_BPPM2 | Q9XJR3 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:252
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
          SPIKE_BPPM2    84 QEQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIKSPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeee....eeee.....eeeeeee....eeee.....hhhhh....eee....eeee.....eeee......eeee............hhhhhhhh....eeeeehhhhh...eeeeeeeee...hhhhh.....eee.eeeeee........eeeee...eee....hhhhheeeeeee....eeeeeeeee...hhhhhhhhh........eeeeeeee.hhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vve A  84 QEQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIKSPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
                                    93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with SPIKE_BPPM2 | Q9XJR3 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:251
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
          SPIKE_BPPM2    85 EQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIKSPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee....eeee.....eeeeeee....eeee....eee..eee..eee....eeee.....eeee......eeee............hhhhhhhh....eeeeehhhhh...eeeeeeeee...hhhhh.....eee.eeeeee........eeee..eeeee..........eeeeee....eeeeeeeee...hhhhhhhhh........eeeeeeee.hhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vve B  85 EQTTKSRDVNSFQIPLRDGVRELLPEDASRNRASIKSPVDIWIGGENMTALNGIVDGGRKFEAGQEFQINTFGSVNYWVSDEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKGYAQILMERT 335
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   Legend:   → Mismatch (orange background)
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  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 2VVE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VVE)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPIKE_BPPM2 | Q9XJR3)
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_BPPM2 | Q9XJR3: 2vvd 2w0c

(-) Related Entries Specified in the PDB File

2vvd CRYSTAL STRUCTURE OF THE RECEPTOR BINDING DOMAIN OF THE SPIKE PROTEIN P1 FROM BACTERIOPHAGE PM2
2w0c X-RAY STRUCTURE OF THE ENTIRE LIPID- CONTAINING BACTERIOPHAGE PM2