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(-) Description

Title :  SOLID-STATE NMR STRUCTURE OF THE M2 TRANSMEMBRANE PEPTIDE OF THE INFLUENZA A VIRUS IN DMPC LIPID BILAYERS BOUND TO DEUTERATED AMANTADINE
 
Authors :  S. D. Cady, K. Schmidt-Rohr, J. Wang, C. S. Soto, W. F. Degrado, M. Hong
Date :  18 Nov 09  (Deposition) - 09 Feb 10  (Release) - 26 Oct 11  (Revision)
Method :  SOLID-STATE NMR
Resolution :  NOT APPLICABLE
Chains :  Asym. Unit :  A,B,C,D  (17x)
Biol. Unit 1:  A,B,C,D  (1x)
Keywords :  Influenza, Transmembrane, Amantadine, Redor, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Cady, K. Schmidt-Rohr, J. Wang, C. Soto, W. F. Degrado, M. Hong
Structure Of The Amantadine Binding Site Of Influenza M2 Proton Channels In Lipid Bilayers
Nature V. 463 689 2010
PubMed-ID: 20130653  |  Reference-DOI: 10.1038/NATURE08722

(-) Compounds

Molecule 1 - M2 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Fragment: RESIDUES 22-46
    Other Details: SOLID-PHASE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit (17x): ABCD
Biological Unit 1 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
13081Ligand/Ion(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13081Ligand/Ion(3S,5S,7S)-TRICYCLO[3.3.1.1~3,7~]DECAN-1-AMINE

(-) Sites  (0, 0)

(no "Site" information available for 2KQT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KQT)

(-) 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:25
 aligned with M2_I97A1 | O70632 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:25
                                    31        41     
              M2_I97A1   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt A 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain A from PDB  Type:PROTEIN  Length:25
 aligned with Q9YP62_9INFA | Q9YP62 from UniProtKB/TrEMBL  Length:97

    Alignment length:25
                                    31        41     
          Q9YP62_9INFA   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt A 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain B from PDB  Type:PROTEIN  Length:25
 aligned with M2_I97A1 | O70632 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:25
                                    31        41     
              M2_I97A1   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt B 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain B from PDB  Type:PROTEIN  Length:25
 aligned with Q9YP62_9INFA | Q9YP62 from UniProtKB/TrEMBL  Length:97

    Alignment length:25
                                    31        41     
          Q9YP62_9INFA   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt B 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain C from PDB  Type:PROTEIN  Length:25
 aligned with M2_I97A1 | O70632 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:25
                                    31        41     
              M2_I97A1   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt C 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain C from PDB  Type:PROTEIN  Length:25
 aligned with Q9YP62_9INFA | Q9YP62 from UniProtKB/TrEMBL  Length:97

    Alignment length:25
                                    31        41     
          Q9YP62_9INFA   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt C 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain D from PDB  Type:PROTEIN  Length:25
 aligned with M2_I97A1 | O70632 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:25
                                    31        41     
              M2_I97A1   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
           Pfam domains (1) Flu_M2-2kqtD01 D:22-46    Pfam domains (1)
           Pfam domains (2) Flu_M2-2kqtD02 D:22-46    Pfam domains (2)
           Pfam domains (3) Flu_M2-2kqtD03 D:22-46    Pfam domains (3)
           Pfam domains (4) Flu_M2-2kqtD04 D:22-46    Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt D 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41     


Chain D from PDB  Type:PROTEIN  Length:25
 aligned with Q9YP62_9INFA | Q9YP62 from UniProtKB/TrEMBL  Length:97

    Alignment length:25
                                    31        41     
          Q9YP62_9INFA   22 SSDPLVVAASIIGILHLILWILDRL 46
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
           Pfam domains (1) Flu_M2-2kqtD01 D:22-46    Pfam domains (1)
           Pfam domains (2) Flu_M2-2kqtD02 D:22-46    Pfam domains (2)
           Pfam domains (3) Flu_M2-2kqtD03 D:22-46    Pfam domains (3)
           Pfam domains (4) Flu_M2-2kqtD04 D:22-46    Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                  2kqt D 22 SSDPLVVAASIIGILHLILWILDRL 46
                                    31        41
   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 2KQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flu_M2] (9)

(-) Gene Ontology  (18, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (M2_I97A1 | O70632)
molecular function
    GO:0015078    hydrogen ion transmembrane transporter activity    Enables the transfer of hydrogen ions from one side of a membrane to the other.
    GO:0005216    ion channel activity    Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
biological process
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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:0039707    pore formation by virus in membrane of host cell    The aggregation, arrangement and bonding together of a set of components by a virus to form a pore complex in a membrane of a host organism.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0039521    suppression by virus of host autophagy    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of autophagy in the host.
    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: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.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0044385    integral to membrane of host cell    Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane. Occurring in a host cell.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain A,B,C,D   (Q9YP62_9INFA | Q9YP62)
molecular function
    GO:0015078    hydrogen ion transmembrane transporter activity    Enables the transfer of hydrogen ions from one side of a membrane to the other.
biological process
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0039521    suppression by virus of host autophagy    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of autophagy in the host.
    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: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.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        M2_I97A1 | O70632: 2kad 3c9j 3lbw 4rwb 4rwc
        Q9YP62_9INFA | Q9YP62: 3lbw
UniProtKB/TrEMBL
        Q9YP62_9INFA | Q9YP62: 2ljb 2ljc

(-) Related Entries Specified in the PDB File

1nyj THE CLOSED STATE STRUCTURE OF M2 PROTEIN H+ CHANNEL BY SOLID STATE NMR SPECTROSCOPY
2h95 STRUCTURE OF THE AMANTADINE-BLOCKED INFLUENZA A M2 PROTON CHANNEL TRANS-MEMBRANE DOMAIN BY SOLID-STATE NMR SPECTROSCOPY
2kad MAGIC-ANGLE-SPINNING SOLID-STATE NMR STRUCTURE OF INFLUENZA A M2 TRANSMEMBRANE DOMAIN
2rlf PROTON CHANNEL M2 FROM INFLUENZA A IN COMPLEX WITH INHIBITOR RIMANTADINE
3bkd HIGH RESOLUTION CRYSTAL STRUCTURE OF TRANSMEMBRANE DOMAIN OF M2 PROTEIN RELATED ID: 16612 RELATED DB: BMRB
3c9j THE CRYSTAL STRUCTURE OF TRANSMEMBRANE DOMAIN OF M2 PROTEIN AND AMANTADINE COMPLEX