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(-) Description

Title :  CRYSTAL STRUCTURE OF YBR137W PROTEIN
 
Authors :  Y. -H. Yeh, T. -W. Lin, C. -Y. Lin, C. -D. Hsiao
Date :  14 Jan 14  (Deposition) - 19 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Protein Transport, Get, Get Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yeh, T. Lin, Y. Li, J. Tung, C. Lin, C. Hsiao
Structural And Functional Characterization Of Ybr137Wp Implicate Its Involvement In The Targeting Of Tail-Anchored Proteins To Membranes.
Mol. Cell. Biol. V. 34 4500 2014
PubMed-ID: 25288638  |  Reference-DOI: 10.1128/MCB.00697-14
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0303 PROTEIN YBR137W
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 2 - UPF0303 PROTEIN YBR137W
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 3 - UPF0303 PROTEIN YBR137W
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 4 - UPF0303 PROTEIN YBR137W
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 5 - UPF0303 PROTEIN YBR137W
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: ESCHERICHIA COLI
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4CLC)

(-) Sites  (0, 0)

(no "Site" information available for 4CLC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CLC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CLC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CLC)

(-) Exons   (0, 0)

(no "Exon" information available for 4CLC)

(-) 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:169
 aligned with YBY7_YEAST | P38276 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           YBY7_YEAST     2 VVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANE 170
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....................eeeeee.......eeeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clc A   2 VVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMALSSLIAFANE 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with YBY7_YEAST | P38276 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
           YBY7_YEAST     1 MVVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANE 170
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh....hhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhh......................eeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clc B   1 MVVLDKKLLERLTSRKVPLEELEDMEKKCFLSTFTYQDAFDLGTYIKNAVKENFPDKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSTYPYACLTISGLKQEEDHLMAVSSLIAFANE 170
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170


Chain C from PDB  Type:PROTEIN  Length:174
 aligned with YBY7_YEAST | P38276 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           YBY7_YEAST     1 MVVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLEE 174
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeeee......hhhhhhhhhhhhhhhhhh.hhhhhhhhhh..hhhhhhh.hhhhhh....eeeeee.......eeeeee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4clc C   1 MVVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLEE 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with YBY7_YEAST | P38276 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
           YBY7_YEAST     1 MVVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLE 173
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeeee.......hhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhh............eeeeee.......eeeeee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clc D   1 MVVLDKKLLERLTSRKVPLEQLEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLE 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   


Chain E from PDB  Type:PROTEIN  Length:173
 aligned with YBY7_YEAST | P38276 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
           YBY7_YEAST     1 MVVLDKKLLERLTSRKVPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLE 173
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhh............eeeeee.......eeeeee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4clc E   1 MVVLDKKLLERLTSRKTPLEELEDMEKRCFLSTFTYQDAFDLGTYIRNAVKENFPEKPVAIDISLPNGHCLFRTVTYGGSALDNDFWIQRKKKTALRFGHSSFYMGCKKGDKTPEEKFFVDSKEYAFHGGAVLIQSERSDYPYACLTISGLKQEEDHLMAVSSLIAFANESLE 173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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 4CLC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CLC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CLC)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (YBY7_YEAST | P38276)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0006620    posttranslational protein targeting to endoplasmic reticulum membrane    The targeting of proteins to a membrane that occurs after their translation. Some secretory proteins exhibit posttranslational transport into the endoplasmic reticulum (ER) lumen: they are synthesized in their entirety on free cytosolic ribosomes and then released into the cytosol, where they are bound by chaperones which keep them in an unfolded state, and subsequently are translocated across the ER membrane.
cellular component
    GO:0072380    TRC complex    An ER membrane insertion complex that contains subunits that recognize two types of transmembrane domain signals. In budding yeast the complex contains Get4p, Get5p, Sgt2p, and at least two heat shock proteins (HSPs).
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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