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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF SYD
 
Authors :  R. Maurus, G. D. Brayer
Date :  04 Dec 08  (Deposition) - 27 Jan 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Membrane, Translocon, Secyeg, Syd, Nanodisc, Cell Inner Membrane, Cell Membrane, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Dalal, N. Nguyen, M. Alami, J. Tan, T. F. Moraes, W. C. Lee, R. Maurus, S. S. Sligar, G. D. Brayer, F. Duong
Structure, Binding, And Activity Of Syd, A Secy-Interacting Protein
J. Biol. Chem. V. 284 7897 2009
PubMed-ID: 19139097  |  Reference-DOI: 10.1074/JBC.M808305200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN SYD
    Chains: A, B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3FFV)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:147 -A:154
2B:1147 -B:1154

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FFV)

(-) 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:181
 aligned with SYDP_ECOLI | P0A8U0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
          SYDP_ECOLI      1 MDDLTAQALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKPLL  181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...ee..........eeee....eee..ee......hhhhhhhh....hhhhhhhh..ee...eeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeee.....eeeee.....eeeee.hhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ffv A    1 MDDLTAQALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKPLL  181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with SYDP_ECOLI | P0A8U0 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
          SYDP_ECOLI      1 MDDLTAQALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKPLL  181
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh...ee..........eeee....eee..ee......hhhhhhhhh...hhhhhhhhhhee...eeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeee.....eeeee.....eeeee.hhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ffv B 1001 MDDLTAQALKDFTARYCDAWHEEHKSWPLSEELYGVPSPCIISTTEDAVYWQPQPFTGEQNVNAVERAFDIVIQPTIHTFYTTQFAGDMHAQFGDIKLTLLQTWSEDDFRRVQENLIGHLVTQKRLKLPPTLFIATLEEELEVISVCNLSGEVCKETLGTRKRTHLASNLAEFLNQLKPLL 1181
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180
   Legend:   → Mismatch (orange background)
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  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 3FFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYDP_ECOLI | P0A8U0)
molecular function
    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:0043254    regulation of protein complex assembly    Any process that modulates the frequency, rate or extent of protein complex assembly.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
    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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