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(-) Description

Title :  THE SOLUTION STRUCTURE OF THE SECOND THIOREDOXIN DOMAIN OF HUMAN PROTEIN DISULFIDE-ISOMERASE A3
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Apr 06  (Deposition) - 22 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Disulfide Isomerase Er-60, Erp60, 58 Kda Microsomal Protein, P58, Erp57, 58 Kda Glucose-Regulated Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Second Thioredoxin Domain Of Human Protein Disulfide-Isomerase A3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DISULFIDE-ISOMERASE A3
    ChainsA
    EC Number5.3.4.1
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050627-10
    Expression System Vector TypePLASMID
    FragmentTHIOREDOXIN DOMAIN
    GenePDIA3, ERP60, GRP58
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymDISULFIDE ISOMERASE ER-60, ERP60, 58 KDA MICROSOMAL PROTEIN, P58, ERP57, 58 KDA GLUCOSE-REGULATED PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DMM)

(-) Sites  (0, 0)

(no "Site" information available for 2DMM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DMM)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:94 -Pro A:95
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:101 -Pro A:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020027K415RPDIA3_HUMANPolymorphism6413485AK66R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PDIA3_HUMAN19-133
343-485
  1-
A:8-136
2THIOREDOXIN_1PS00194 Thioredoxin family active site.PDIA3_HUMAN49-67
398-416
  1-
A:49-67

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003002891aENSE00001489318chr15:44038590-44038904315PDIA3_HUMAN1-56560--
1.4ENST000003002894ENSE00001782278chr15:44046022-4404610079PDIA3_HUMAN56-82270--
1.5bENST000003002895bENSE00001672356chr15:44048847-44048964118PDIA3_HUMAN83-122400--
1.6ENST000003002896ENSE00001792513chr15:44053622-44053729108PDIA3_HUMAN122-158370--
1.7ENST000003002897ENSE00001692828chr15:44055275-44055404130PDIA3_HUMAN158-201440--
1.8ENST000003002898ENSE00001623236chr15:44057648-44057764117PDIA3_HUMAN201-240400--
1.9ENST000003002899ENSE00001747426chr15:44058085-44058210126PDIA3_HUMAN240-282430--
1.10ENST0000030028910ENSE00001667287chr15:44058926-44059108183PDIA3_HUMAN282-343621A:1-77
1.11bENST0000030028911bENSE00001777596chr15:44060687-44060795109PDIA3_HUMAN343-379371A:8-3023
1.12ENST0000030028912ENSE00001667800chr15:44061716-44061844129PDIA3_HUMAN380-422431A:31-7343
1.13aENST0000030028913aENSE00001768045chr15:44062448-4406252780PDIA3_HUMAN423-449271A:74-10027
1.13cENST0000030028913cENSE00001782281chr15:44062721-4406277858PDIA3_HUMAN449-468201A:100-11920
1.14bENST0000030028914bENSE00001145733chr15:44063303-440654772175PDIA3_HUMAN469-505371A:120-14223

(-) Sequences/Alignments

NMR Structure
   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:142
 aligned with PDIA3_HUMAN | P30101 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:177
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          PDIA3_HUMAN   315 GLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALERFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELGEKLSKDPNIVIAKMDATANDVPSPYEVRGFPTIYFSPANKKLNPKKYEGGRELSDFISYLQREATNPPVIQ 491
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......-----------------------------------......................ee.hhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeee.................eeeee...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------R---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------THIOREDOXIN_2  PDB: A:8-136 UniProt: 343-485                                                                                                   ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------THIOREDOXIN_1      --------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: A:1-7        ------------------------------------Exon 1.12  PDB: A:31-73 UniProt: 380-422   Exon 1.13a  PDB: A:74-100  -------------------Exon 1.14b [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.11b  PDB: A:8-30 [INCOMPLETE] ---------------------------------------------------------------------Exon 1.13c          ----------------------- Transcript 1 (2)
                 2dmm A   1 GSSGSSG-----------------------------------FDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELGEKLSKDPNIVIAKMDATANDVPSPYEVRGFPTIYFSPANKKLNPKKYEGGRELSDFISYLQREATSGPSSG 142
                                  |  -         -         -         -  |     15        25        35        45        55        65        75        85        95       105       115       125       135       
                                  7                                   8                                                                                                                                      

   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 2DMM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DMM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

NMR Structure(hide GO term definitions)
Chain A   (PDIA3_HUMAN | P30101)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004629    phospholipase C activity    Catalysis of the reaction: a phospholipid + H2O = 1,2-diacylglycerol + a phosphatidate.
    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:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:2001238    positive regulation of extrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    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:0034975    protein folding in endoplasmic reticulum    A protein folding process that takes place in the endoplasmic reticulum (ER). Secreted, plasma membrane and organelle proteins are folded in the ER, assisted by chaperones and foldases (protein disulphide isomerases), and additional factors required for optimal folding (ATP, Ca2+ and an oxidizing environment to allow disulfide bond formation).
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0006621    protein retention in ER lumen    The retention in the endoplasmic reticulum (ER) lumen of soluble resident proteins. Sorting receptors retrieve proteins with ER localization signals, such as KDEL and HDEL sequences or some transmembrane domains, that have escaped to the cis-Golgi network and return them to the ER. Abnormally folded proteins and unassembled subunits are also selectively retained in the ER.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        PDIA3_HUMAN | P301012alb 2h8l 3f8u

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