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(-) Description

Title :  STRUCTURE AND FUNCTION OF A MEMBRANE COMPONENT SECDF THAT ENHANCES PROTEIN EXPORT
 
Authors :  Y. Echizen, T. Tsukazaki, R. Ishitani, O. Nureki
Date :  16 Nov 10  (Deposition) - 18 May 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Periplasmic Domain, Secdf, Sec, Translocon, Cell Membrane, Membrane, Protein Transport, Translocation, Transmembrane, Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tsukazaki, H. Mori, Y. Echizen, R. Ishitani, S. Fukai, T. Tanaka, A. Perederina, D. G. Vassylyev, T. Kohno, A. D. Maturana, K. Ito, O. Nureki
Structure And Function Of A Membrane Component Secdf That Enhances Protein Export.
Nature V. 474 235 2011
PubMed-ID: 21562494  |  Reference-DOI: 10.1038/NATURE09980
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE SECDF PROTEIN-EXPORT MEMBRANE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-26B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SECDF P1 DOMAIN (UNP RESIDUES 35-263)
    Gene: SECDF, TTHA0697
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3AQO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AQO)

(-) Exons   (0, 0)

(no "Exon" information available for 3AQO)

(-) 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:221
 aligned with SECDF_THET8 | Q5SKE6 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:221
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 
          SECDF_THET8    42 GLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhhh....eeeee...eeeeee...hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhh....hhhhhhh...hhhhh....ee...eeeeeeee.....eeeeeeehhhhhhhhhhhhhhh....eeeee..eeee...........eeee....hhhhhhhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqo A  42 GLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with SECDF_THET8 | Q5SKE6 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:220
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262
          SECDF_THET8    43 LRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhhhh....eeeee...eeeee....hhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhh...hhhhhhh...hhh.eeeeeee...eeeeeeee.....eeeeeeehhhhhhhhhhhhhhh....eeeee..eeee...........eeee....hhhhhhhhhhhhhhh.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqo B  43 LRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262


Chain C from PDB  Type:PROTEIN  Length:222
 aligned with SECDF_THET8 | Q5SKE6 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:222
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
          SECDF_THET8    41 GGLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee...eeeeee...hhhhhhhhhhhhh....eeeee........hhhhhhhhhhhh...hhhhhhh...hhhhh....ee...eeeeeeee.....eeeeeeehhhhhhhhhhhhhhh....eeeee..eeee...........eeee....hhhhhhhhhhhhhh......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3aqo C  41 GGLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  


Chain D from PDB  Type:PROTEIN  Length:221
 aligned with SECDF_THET8 | Q5SKE6 from UniProtKB/Swiss-Prot  Length:735

    Alignment length:221
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 
          SECDF_THET8    42 GLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee...eeeeee...hhhhhhhhhhhhh....eeeee........hhhhhhhhhhhh...hhhhhhh...hhhhh....ee...eeeeeeee.....eeeeeeehhhhhhhhhhhhhhhh...eeeee..eeee...........eeee....hhhhhhhhhhhhhhh.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqo D  42 GLRIVLEADVENPTLDDLEKARTVLENRINALGVAEPLIQIQGQKRIVVELPGLSQADQDRALKLIGQRAVLEFRIVKEGATGTTVAQINQALRENPRLNREELEKDLIKPEDLGPPLLTGADLADARAVFDQFGRPQVSLTFTPEGAKKFEEVTRQNIGKRLAIVLDGRVYTAPVIRQAITGGQAVIEGLSSVEEASEIALVLRSGSLPVPLKVAEIRAI 262
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 3AQO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AQO)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SECDF_THET8 | Q5SKE6)
molecular function
    GO:0015450    P-P-bond-hydrolysis-driven protein transmembrane transporter activity    Primary active carrier-mediated transport of a protein across a membrane, driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated.
biological process
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0071806    protein transmembrane transport    The directed movement of a protein across a membrane by means of some agent such as a transporter or pore.
    GO:0015031    protein transport    The directed movement of proteins 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.
cellular component
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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        SECDF_THET8 | Q5SKE6: 2rrn 3aqp

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