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(-) Description

Title :  CRYSTAL STRUCTURE OF YIDC FROM BACILLUS HALODURANS (FORM II)
 
Authors :  K. Kumazaki, T. Tsukazaki, R. Ishitani, O. Nureki
Date :  20 Dec 13  (Deposition) - 23 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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 27-267
    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

  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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CU4Ligand/IonCOPPER (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:34 , GLU A:95 , HIS A:128BINDING SITE FOR RESIDUE CU A 301
2AC2SOFTWAREHIS A:39 , GLU A:266 , GLU A:269BINDING SITE FOR RESIDUE CU A 302
3AC3SOFTWAREGLU B:34 , GLU B:95 , HIS B:128BINDING SITE FOR RESIDUE CU B 301
4AC4SOFTWAREHIS B:39 , GLU B:269BINDING SITE FOR RESIDUE CU B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WO7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WO7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WO7)

(-) Exons   (0, 0)

(no "Exon" information available for 3WO7)

(-) 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:224
 aligned with YIDC2_BACHD | Q9KDP2 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:246
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      
          YIDC2_BACHD    27 DPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKGSKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMSHQQQMQKTNPSDSDNPMANMMQMQMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTYFIVVKAPPLEVEQTKQ 272
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee......hhhhhhhhhhhhhhhhhh..----------------------.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wo7 A  27 DPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKASKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMSH----------------------QMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTYFIVVKAPPLEVLESSG 272
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       | -         -         -|      226       236       246       256       266      
                                                                                                                                                                                                 194                    217                                                       


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with YIDC2_BACHD | Q9KDP2 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:246
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      
          YIDC2_BACHD    27 DPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKGSKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMSHQQQMQKTNPSDSDNPMANMMQMQMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTYFIVVKAPPLEVEQTKQ 272
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee......hhhhhhhhhhhhhhhhhhh---------------------.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wo7 B  27 DPITSESEGIWNHFFVYPMSWLITTVANLLNGSYGLSIIIVTILIRLALLPLTLKQQKSMRAMQVIRPEMEAIQKKYKEKASKDPKVQQEMQKELLGLYQKHGVNPMAGCLPLFIQLPILMAFYFAIMRTEEIRYHTFLWFDLGQPDYILPFVAGITTYFQFKMTMS---------------------QMQMKVMLYVMPVMIIIAGLSLPSALSLYWVIGNIFMIIQTYFIVVKAPPLEVLESSG 272
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186      |  -         -       216       226       236       246       256       266      
                                                                                                                                                                                                193                   215
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3WO7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WO7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WO7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3wo7
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  YIDC2_BACHD | Q9KDP2
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 Related Entries

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

UniProtKB/Swiss-Prot
        YIDC2_BACHD | Q9KDP2: 3wo6

(-) Related Entries Specified in the PDB File

3w06