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(-) Description

Title :  CRYSTAL STRUCTURE OF TRX4 DOMAIN OF ERDJ5
 
Authors :  K. Inaba, M. Suzuki, K. Nagata
Date :  20 Oct 10  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thioredoxin Fold, Cxxc Motif, Endoplasmic Reticulum, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hagiwara, K. Maegawa, M. Suzuki, R. Ushioda, K. Araki, Y. Matsumoto J. Hoseki, K. Nagata, K. Inaba
Structural Basis Of An Erad Pathway Mediated By The Er-Resident Protein Disulfide Reductase Erdj5.
Mol. Cell V. 41 432 2011
PubMed-ID: 21329881  |  Reference-DOI: 10.1016/J.MOLCEL.2011.01.021

(-) Compounds

Molecule 1 - DNAJ HOMOLOG SUBFAMILY C MEMBER 10
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOLD-TF
    Expression System StrainORIGAMI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTRX4 DOMAIN (UNP RESIDUES 668-789)
    GeneDNAJC10, ERDJ5, JPDI
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymER-RESIDENT PROTEIN ERDJ5, ENDOPLASMIC RETICULUM DNAJ-PDI FUSION PROTEIN 1

 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
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:677 , TYR A:731 , PRO A:732 , GLN A:733 , THR A:734BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREALA A:742 , TYR A:743BINDING SITE FOR RESIDUE GOL A 790

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:700 -A:703
2A:728 -A:735
3B:700 -B:703
4B:728 -B:735

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:743 -Pro A:744
2Tyr B:743 -Pro B:744

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DJC10_MOUSE472-490
692-710
 
  2-
A:692-710
B:692-710
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DJC10_MOUSE472-490
692-710
 
  1-
A:692-710
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DJC10_MOUSE472-490
692-710
 
  1-
-
B:692-710

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000283921ENSMUSE00000477397chr2:80155623-80155962340DJC10_MOUSE-00--
1.2ENSMUST000000283922ENSMUSE00000889499chr2:80157406-80157756351DJC10_MOUSE1-68680--
1.3ENSMUST000000283923ENSMUSE00000165366chr2:80159317-80159479163DJC10_MOUSE69-123550--
1.4ENSMUST000000283924ENSMUSE00000165373chr2:80161401-8016145151DJC10_MOUSE123-140180--
1.5aENSMUST000000283925aENSMUSE00000403421chr2:80164817-8016489983DJC10_MOUSE140-167280--
1.6ENSMUST000000283926ENSMUSE00000165376chr2:80165152-80165283132DJC10_MOUSE168-211440--
1.7ENSMUST000000283927ENSMUSE00000165375chr2:80165775-8016586894DJC10_MOUSE212-243320--
1.8ENSMUST000000283928ENSMUSE00000165370chr2:80166815-8016689278DJC10_MOUSE243-269270--
1.9ENSMUST000000283929ENSMUSE00000240006chr2:80168229-8016827244DJC10_MOUSE269-283150--
1.10aENSMUST0000002839210aENSMUSE00000239999chr2:80171426-80171563138DJC10_MOUSE284-329460--
1.11aENSMUST0000002839211aENSMUSE00000165371chr2:80173086-8017317590DJC10_MOUSE330-359300--
1.11dENSMUST0000002839211dENSMUSE00000165379chr2:80173883-80173996114DJC10_MOUSE360-397380--
1.12ENSMUST0000002839212ENSMUSE00000165377chr2:80175610-80175724115DJC10_MOUSE398-436390--
1.13ENSMUST0000002839213ENSMUSE00000165369chr2:80180630-80180757128DJC10_MOUSE436-478430--
1.14bENSMUST0000002839214bENSMUSE00000239958chr2:80180969-80181085117DJC10_MOUSE479-517390--
1.15ENSMUST0000002839215ENSMUSE00000239949chr2:80184074-80184175102DJC10_MOUSE518-551340--
1.16ENSMUST0000002839216ENSMUSE00000428676chr2:80185081-80185236156DJC10_MOUSE552-603520--
1.17ENSMUST0000002839217ENSMUSE00000239906chr2:80186669-80186802134DJC10_MOUSE604-648450--
1.18ENSMUST0000002839218ENSMUSE00000239898chr2:80187501-8018755454DJC10_MOUSE648-666190--
1.19aENSMUST0000002839219aENSMUSE00000239888chr2:80187805-80187952148DJC10_MOUSE666-715502A:669-715
B:669-715
47
47
1.20ENSMUST0000002839220ENSMUSE00000239880chr2:80189426-80189545120DJC10_MOUSE716-755402A:716-755
B:716-755
40
40
1.21aENSMUST0000002839221aENSMUSE00000413886chr2:80190786-80190890105DJC10_MOUSE756-790352A:756-782
B:756-782
27
27
1.22ENSMUST0000002839222ENSMUSE00000688937chr2:80193016-801942001185DJC10_MOUSE791-79330--

(-) 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:114
 aligned with DJC10_MOUSE | Q9DC23 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:114
                                   678       688       698       708       718       728       738       748       758       768       778    
          DJC10_MOUSE   669 PQASIDLTPQTFNEKVLQGKTHWVVDFYAPWCGPCQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLETL 782
               SCOP domains d3apsa_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeeeeehhhheeeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.19a  PDB: A:669-715 UniProt: 666-715    Exon 1.20  PDB: A:716-755               Exon 1.21a  PDB: A:756-782  Transcript 1
                 3aps A 669 PQASIDLTPQTFNEKVLQGKTHWVVDFYAPWCGPCQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLETL 782
                                   678       688       698       708       718       728       738       748       758       768       778    

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with DJC10_MOUSE | Q9DC23 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:114
                                   678       688       698       708       718       728       738       748       758       768       778    
          DJC10_MOUSE   669 PQASIDLTPQTFNEKVLQGKTHWVVDFYAPWCGPCQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLETL 782
               SCOP domains d3apsb_ B: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhhhhhh......eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeeeee....eeeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.19a  PDB: B:669-715 UniProt: 666-715    Exon 1.20  PDB: B:716-755               Exon 1.21a  PDB: B:756-782  Transcript 1
                 3aps B 669 PQASIDLTPQTFNEKVLQGKTHWVVDFYAPWCGPCQNFAPEFELLARMIKGKVRAGKVDCQAYPQTCQKAGIKAYPSVKLYQYERAKKSIWEEQINSRDAKTIAALIYGKLETL 782
                                   678       688       698       708       718       728       738       748       758       768       778    

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DJC10_MOUSE | Q9DC23)
molecular function
    GO:0001671    ATPase activator activity    Binds to and increases the ATP hydrolysis activity of an ATPase.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0015036    disulfide oxidoreductase activity    Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
    GO:0051787    misfolded protein binding    Interacting selectively and non-covalently with a misfolded protein.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0070059    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to a stimulus indicating endoplasmic reticulum (ER) stress, and ends when the execution phase of apoptosis is triggered. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    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:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    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: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:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    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:0034663    endoplasmic reticulum chaperone complex    A protein complex that is located in the endoplasmic reticulum and is composed of chaperone proteins, including BiP, GRP94; CaBP1, protein disulfide isomerase (PDI), ERdj3, cyclophilin B, ERp72, GRP170, UDP-glucosyltransferase, and SDF2-L1.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DJC10_MOUSE | Q9DC233apo 3apq 5ayk 5ayl

(-) Related Entries Specified in the PDB File

3apo CRYSTAL STRUCTURE OF FULL-LENGTH ERDJ5
3apq CRYSTAL STRUCTURE OF J-TRX1 FRAGMENT OF ERDJ5