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(-) Description

Title :  THE HOST OUTER MEMBRANE PROTEINS OMPA AND OMPC ARE PACKED AT SPECIFIC SITES IN THE SHIGELLA PHAGE SF6 VIRION AS STRUCTURAL COMPONENTS
 
Authors :  H. Zhao, R. D. Sequeira, N. A. Galeva, L. Tang
Date :  02 Jun 10  (Deposition) - 16 Feb 11  (Release) - 09 Nov 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  19.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (60x)
Keywords :  Virus Assembly, Cementing Protein, Bacteriophage, Sf6, Shigella, Beta-Barrel, Outer Membrane Protein, Icosahedral, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhao, R. D. Sequeira, N. A. Galeva, L. Tang
The Host Outer Membrane Proteins Ompa And Ompc Are Associated With The Shigella Phage Sf6 Virion.
Virology V. 409 319 2011
PubMed-ID: 21071053  |  Reference-DOI: 10.1016/J.VIROL.2010.10.030

(-) Compounds

Molecule 1 - OUTER MEMBRANE PROTEIN A
    ChainsA, B, C
    FragmentOUTER MEMBRANE PROTEIN A
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymOUTER MEMBRANE PROTEIN II*
 
Molecule 2 - OUTER MEMBRANE PROTEIN C
    ChainsD
    FragmentOUTER MEMBRANE PROTEIN C
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12
    SynonymPORIN OMPC, OUTER MEMBRANE PROTEIN 1B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (60x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NB3)

(-) Sites  (0, 0)

(no "Site" information available for 3NB3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NB3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NB3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRAM_NEG_PORINPS00576 General diffusion Gram-negative porins signature.OMPC_ECOLI319-335  1D:298-314
Biological Unit 1 (1, 60)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRAM_NEG_PORINPS00576 General diffusion Gram-negative porins signature.OMPC_ECOLI319-335  60D:298-314

(-) Exons   (0, 0)

(no "Exon" information available for 3NB3)

(-) 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:137
 aligned with OMPA_ECOLI | P0A910 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           OMPA_ECOLI    22 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG 192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee.-------------...eeeeeeeeeeeee..eeeeeeeeeeee...-------.eeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeee.--------------.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb3 A   1 APKDNTWYTGAKLGWSQ-------------HENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPY-------AYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTN--------------GMLSLGVSYRFG 171
                                    10      |  -         -|       40        50        60  |      -|       80        90       100       110       120       130       140    |    -       160       170 
                                           17            31                              63      71                                                                       145            160           

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with OMPA_ECOLI | P0A910 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           OMPA_ECOLI    22 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG 192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee.-------------...eeeeeeeeeeeee..eeeeeeeeeeee...-------.eeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeee.--------------.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb3 B   1 APKDNTWYTGAKLGWSQ-------------HENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPY-------AYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTN--------------GMLSLGVSYRFG 171
                                    10      |  -         -|       40        50        60  |      -|       80        90       100       110       120       130       140    |    -       160       170 
                                           17            31                              63      71                                                                       145            160           

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with OMPA_ECOLI | P0A910 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:171
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
           OMPA_ECOLI    22 APKDNTWYTGAKLGWSQYHDTGFINNNGPTHENQLGAGAFGGYQVNPYVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTKSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTNNIGDAHTIGTRPDNGMLSLGVSYRFG 192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -OmpA_membrane-3n             b3C01 C:2-171                                                                                                                                 Pfam domains (1)
           Pfam domains (2) -OmpA_membrane-3n             b3C02 C:2-171                                                                                                                                 Pfam domains (2)
           Pfam domains (3) -OmpA_membrane-3n             b3C03 C:2-171                                                                                                                                 Pfam domains (3)
         Sec.struct. author .....eeeeeeeeeee.-------------...eeeeeeeeeeeee..eeeeeeeeeeee...-------.eeeeeeeeeeeeeee....eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeee..eeeeeeeeee.--------------.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb3 C   1 APKDNTWYTGAKLGWSQ-------------HENKLGAGAFGGYQVNPYVGFEMGYDWLGRMPY-------AYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGVSPVFAGGVEYAITPEIATRLEYQWTN--------------GMLSLGVSYRFG 171
                                    10      |  -         -|       40        50        60  |      -|       80        90       100       110       120       130       140    |    -       160       170 
                                           17            31                              63      71                                                                       145            160           

Chain D from PDB  Type:PROTEIN  Length:346
 aligned with OMPC_ECOLI | P06996 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:346
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361      
           OMPC_ECOLI    22 AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF 367
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Porin_1-3nb3D01 D:6-346                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeeeeeeee.......ee..eeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee...eeeeeeeee..hhhhhhhhh..................eeeeeeeeeeehhhhh...eeeeeeee....................hhhhh...eeeeeeeeee..eeeeeeeeeee...............eeeeeeeeeeeee..eeeeeeeeeee............eeeeeeeeeee.....eeeeeeeeeeeee........eeeeeeeeeeeeee....eeeeeeeeee....hhhhhhhh.....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GRAM_NEG_PORIN   -------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nb3 D   1 AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQIQGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQTYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDVGATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF 346
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340      

   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 3NB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NB3)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: MBB (97)

(-) Gene Ontology  (18, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (OMPA_ECOLI | P0A910)
molecular function
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0009597    detection of virus    The series of events in which a stimulus from a virus is received and converted into a molecular signal.
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019867    outer membrane    The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

Chain D   (OMPC_ECOLI | P06996)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0045203    integral component of cell outer membrane    The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        OMPA_ECOLI | P0A9101bxw 1g90 1qjp 2ge4 2jmm 3jbu 5m2q
        OMPC_ECOLI | P069962j1n 2j4u 2zle 4a8d

(-) Related Entries Specified in the PDB File

1qjp HOMOLOGUE OF ONE OF THE TWO HOST-DERIVED CEMENTING PROTEINS THAT ARE PACKED IN THE SF6 VIRION
2j1n HOMOLOGUE OF ONE OF THE TWO HOST-DERIVED CEMENTING PROTEINS THAT ARE PACKED IN THE SF6 VIRION