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(-) Description

Title :  STRUCTURE OF PDI-RELATED CHAPERONE, WIND MUTANT-Y53S
 
Authors :  M. Sevvana, Q. Ma, K. Barnewitz, C. Guo, H. -D. Soling, D. M. Ferrari, G. M. Sheldrick
Date :  02 Sep 05  (Deposition) - 29 Aug 06  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Wind, Windbeutel, Pdi-Dbeta, Pdi, Protein Disulfide Isomerase, Pipe, Dorsal-Ventral Patterning, Chaperone, Wind Mutants, Developmental Protein, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sevvana, M. Biadene, Q. Ma, C. Guo, H. -D. Soling, G. M. Sheldrick, D. M. Ferrari
Structural Elucidation Of The Pdi-Related Chaperone Wind With The Help Of Mutants.
Acta Crystallogr. , Sect. D V. 62 589 2006
PubMed-ID: 16699185  |  Reference-DOI: 10.1107/S0907444906010456
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WINDBEUTEL PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE-30 (QIAGEN)
    Expression System StrainXL1-BLUE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymERP29 HOMOLOG

 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:1179 , GLN A:1188 , ARG A:1192 , HOH A:2079BINDING SITE FOR RESIDUE NA A2252
2AC2SOFTWARELEU B:1033 , GLU B:1036 , LYS B:1037 , HOH B:2005BINDING SITE FOR RESIDUE CL B2245

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:1024 -A:1027
2B:1024 -B:1027

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:1105 -Pro A:1106
2Phe B:1105 -Pro B:1106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2C0G)

(-) Exons   (0, 0)

(no "Exon" information available for 2C0G)

(-) 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:228
 aligned with WBL_DROME | O44342 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:228
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243        
           WBL_DROME     24 CTGCVDLDELSFEKTVERFPYSVVKFDIAYPYGEKHEAFTAFSKSAHKATKDLLIATVGVKDYGELENKALGDRYKVDDKNFPSIFLFKGNADEYVQLPSHVDVTLDNLKAFVSANTPLYIGRDGCIKEFNEVLKNYANIPDAEQLKLIEKLQAKQEQLTDPEQQQNARAYLIYMRKIHEVGYDFLEEETKRLLRLKAGKVTEAKKEELLRKLNILEVFRVHKVTKTA  251
               SCOP domains d2c0ga2 A:1024-1145 automated matches                                                                                     d2c0ga1 A:1146-1251 automated matches                                                                      SCOP domains
               CATH domains 2c0gA01 A:1024-1145 Glutaredoxin                                                                                          2c0gA02 A:1146-1251  [code=1.20.1150.12, no name defined]                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....hhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeee.......hhhhhhhh........eeeee......eee.......hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2c0g A 1024 CTGCVDLDELSFEKTVERFPYSVVKFDIASPYGEKHEAFTAFSKSAHKATKDLLIATVGVKDYGELENKALGDRYKVDDKNFPSIFLFKGNADEYVQLPSHVDVTLDNLKAFVSANTPLYIGRDGCIKEFNEVLKNYANIPDAEQLKLIEKLQAKQEQLTDPEQQQNARAYLIYMRKIHEVGYDFLEEETKRLLRLKAGKVTEAKKEELLRKLNILEVFRVHKVTKTA 1251
                                  1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243        

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with WBL_DROME | O44342 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:221
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 
           WBL_DROME     24 CTGCVDLDELSFEKTVERFPYSVVKFDIAYPYGEKHEAFTAFSKSAHKATKDLLIATVGVKDYGELENKALGDRYKVDDKNFPSIFLFKGNADEYVQLPSHVDVTLDNLKAFVSANTPLYIGRDGCIKEFNEVLKNYANIPDAEQLKLIEKLQAKQEQLTDPEQQQNARAYLIYMRKIHEVGYDFLEEETKRLLRLKAGKVTEAKKEELLRKLNILEVFRV  244
               SCOP domains d2c0gb2 B:1024-1145 automated matches                                                                                     d2c0gb1 B:1146-1244 automated matches                                                               SCOP domains
               CATH domains 2c0gB01 B:1024-1145 Glutaredoxin                                                                                          2c0gB02 B:1146-1244  [code=1.20.1150.12, no name defined]                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhh.......eeeee......eee.......hhhhhhhhhhhhh.........hhhhhh.........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2c0g B 1024 CTGCVDLDELSFEKTVERFPYSVVKFDIASPYGEKHEAFTAFSKSAHKATKDLLIATVGVKDYGELENKALGDRYKVDDKNFPSIFLFKGNADEYVQLPSHVDVTLDNLKAFVSANTPLYIGRDGCIKEFNEVLKNYANIPDAEQLKLIEKLQAKQEQLTDPEQQQNARAYLIYMRKIHEVGYDFLEEETKRLLRLKAGKVTEAKKEELLRKLNILEVFRV 1244
                                  1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243 

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C0G)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (WBL_DROME | O44342)
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).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0008063    Toll signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0009950    dorsal/ventral axis specification    The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0009792    embryo development ending in birth or egg hatching    The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell.
    GO:0007313    maternal specification of dorsal/ventral axis, oocyte, soma encoded    Polarization of the oocyte along the dorsal-ventral axis, by a gene product encoded by somatic cells. An example of this is found in Drosophila melanogaster.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0009306    protein secretion    The controlled release of proteins from a cell.
    GO:0000042    protein targeting to Golgi    The process of directing proteins towards the Golgi; usually uses signals contained within the protein.
    GO:0040014    regulation of multicellular organism growth    Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.

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 Related Entries

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

UniProtKB/Swiss-Prot
        WBL_DROME | O443421ovn 2c0e 2c0f 2c1y

(-) Related Entries Specified in the PDB File

1ovn CRYSTAL STRUCTURE AND FUNCTIONAL ANALYSIS OF DROSOPHILAWIND-- A PDI-RELATED PROTEIN
2c0e STRUCTURE OF PDI-RELATED CHAPERONE, WIND WITH HIS-TAG ON C-TERMINUS.
2c0f STRUCTURE OF WIND Y53F MUTANT
2c1y STRUCTURE OF PDI-RELATED CHAPERONE, WIND MUTANT-Y55K