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(-) Description

Title :  CRYSTAL STRUCTURE OF YIDC FROM BACILLUS HALODURANS (FORM I)
 
Authors :  K. Kumazaki, T. Tsukazaki, R. Ishitani, O. Nureki
Date :  20 Dec 13  (Deposition) - 23 Apr 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha Helical, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kumazaki, S. Chiba, M. Takemoto, A. Furukawa, K. Nishiyama, Y. Sugano, T. Mori, N. Dohmae, K. Hirata, Y. Nakada-Nakura, A. D. Maturana, Y. Tanaka, H. Mori, Y. Sugita, F. Arisaka, K. Ito, R. Ishitani, T. Tsukazaki, O. Nureki
Structural Basis Of Sec-Independent Membrane Protein Insertion By Yidc
Nature 2014
PubMed: search  |  Reference-DOI: 10.1038/NATURE13167

(-) Compounds

Molecule 1 - MEMBRANE PROTEIN INSERTASE YIDC 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET VARIANT
    Expression System Strain: C41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 25-256
    Gene: YIDC2, BH1169
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125
    Synonym: FOLDASE YIDC 2, MEMBRANE INTEGRASE YIDC 2, MEMBRANE PROTEIN YIDC 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:25 , GLU A:116 , HIS A:162 , HOH A:401BINDING SITE FOR RESIDUE CD A 301
2AC2SOFTWARETYR A:185BINDING SITE FOR RESIDUE OLC A 302
3AC3SOFTWARESER A:33 , LEU A:165BINDING SITE FOR RESIDUE OLC A 303
4AC4SOFTWAREPHE A:41 , ILE A:141BINDING SITE FOR RESIDUE OLC A 304
5AC5SOFTWAREGLU A:34 , TRP A:37 , ASN A:38 , PHE A:151 , ARG A:155BINDING SITE FOR RESIDUE OLC A 305
6AC6SOFTWAREGLU A:32 , SER A:33 , ASN A:57BINDING SITE FOR RESIDUE OLC A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WO6)

(-) Exons   (0, 0)

(no "Exon" information available for 3WO6)

(-) Sequences/Alignments

Asymmetric/Biological 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:212
 aligned with YIDC2_BACHD | Q9KDP2 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:232
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
          YIDC2_BACHD    25 TTDPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKGSKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMSHQQQMQKTNPSDSDNPMANMMQMQMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTY 256
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......ee..ee......hhhhhhhhhhhhhhhhhhhh--------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wo6 A  25 GQDPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKASKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMSH--------------------QMQMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTY 256
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194         -         -|      224       234       244       254  
                                                                                                                                                                                                   194                  215
   Legend:   → Mismatch (orange background)
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  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 3WO6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WO6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WO6)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YIDC2_BACHD | Q9KDP2)
biological process
    GO:0051205    protein insertion into membrane    The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.
    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: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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  3wo6
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 Related Entries

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

UniProtKB/Swiss-Prot
        YIDC2_BACHD | Q9KDP2: 3wo7

(-) Related Entries Specified in the PDB File

3wo7