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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 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 :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Viral 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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINF
    Expression System Strain: B834
    Expression System Taxid: 562
    Fragment: RECEPTOR BINDING DOMAIN, RESIDUES 159-335
    Organism Scientific: PSEUDOALTEROMONAS PHAGE PM2
    Organism Taxid: 10661
    Synonym: P1-RECEPTOR BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:232 , ASP A:294 , ASP A:296 , HOH A:2032 , HOH A:2034 , HOH A:2068BINDING SITE FOR RESIDUE CA A1328
2AC2SOFTWAREASP A:166 , GLU A:168 , ASP A:269 , HOH A:2001 , HOH A:2002 , HOH A:2122 , HOH A:2124BINDING SITE FOR RESIDUE CA A1329

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:PROTEIN  Length:162
 aligned with SPIKE_BPPM2 | Q9XJR3 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:162
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324  
          SPIKE_BPPM2   165 DEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVMVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKG 326
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhh....eeeeehhhhh...eeeeeeeee...hhhhh.........eeeeee........eeee...........hhhhheeeeeee....eeeeeeeee...hhhhhhhhh........eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vvd A 166 DEEIRVFKEYSARAKYAQNEGRTALEANNVPFFDIDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVKPAFYITEGDETTDTLIKYTSYGSTGSHSGYDFDDNTLDVmVTLSAGVHRVFPVETELDYDAVQEVQHDWYDESFTTFIEVYSDDPLLTVKG 327
                                   175       185       195       205       215       225       235       245       255       265       275|      285       295       305       315       325  
                                                                                                                                        276-MSE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2VVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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: 2vve 2w0c

(-) Related Entries Specified in the PDB File

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