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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HSP40 HDJ1 PEPTIDE-BINDING DOMAIN
 
Authors :  H. Suzuki, S. Noguchi, Y. Satow
Date :  12 Apr 10  (Deposition) - 23 Feb 11  (Release) - 23 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Suzuki, S. Noguchi, H. Arakawa, T. Tokida, M. Hashimoto, Y. Satow
Peptide-Binding Sites As Revealed By The Crystal Structures Of The Human Hsp40 Hdj1 C-Terminal Domain In Complex With The Octapeptide From Human Hsp70
Biochemistry V. 49 8577 2010
PubMed-ID: 20809635  |  Reference-DOI: 10.1021/BI100876N

(-) Compounds

Molecule 1 - DNAJ HOMOLOG SUBFAMILY B MEMBER 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 161-340
    GeneDNAJB1, DNAJ1, HDJ1, HSPF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEAT SHOCK 40 KDA PROTEIN 1, HEAT SHOCK PROTEIN 40, HSP40, DNAJ PROTEIN HOMOLOG 1, HUMAN DNAJ PROTEIN 1, HDJ-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3AGX)

(-) Sites  (0, 0)

(no "Site" information available for 3AGX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002543221ENSE00000902164chr19:14629201-14628951251DNJB1_HUMAN1-71710--
1.2ENST000002543222ENSE00000902163chr19:14627858-14627278581DNJB1_HUMAN71-2641942A:165-264
B:165-264 (gaps)
100
100
1.3ENST000002543223ENSE00000902162chr19:14626982-146255821401DNJB1_HUMAN265-340762A:265-340
B:265-340
76
76

(-) Sequences/Alignments

Asymmetric/Biological 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:176
 aligned with DNJB1_HUMAN | P25685 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:176
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      
          DNJB1_HUMAN   165 THDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKKGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI 340
               SCOP domains d3agxa1 A:165-245 automated matches                                              d3agxa2 A:246-340 automated matches                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhheeeeeeeeeeee......eeeeeeeeeeee........eeee..............eeeeeee......eee..eeeeeeeeehhhhhhheeeeee.....eeeeee........eeee................eeeeeeee.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:165-264 UniProt: 71-264 [INCOMPLETE]                                               Exon 1.3  PDB: A:265-340 UniProt: 265-340                                    Transcript 1
                 3agx A 165 THDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKKGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI 340
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with DNJB1_HUMAN | P25685 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:176
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      
          DNJB1_HUMAN   165 THDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKKGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI 340
               SCOP domains d3agxb1 B:165-245 aut                  omated matches                            d3agxb2 B:246-340 automated matches                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhheeee...------------------.eeee........eee...----------...eeeeee......eee..eeeeeeeeehhhhhhheeeeee.....eeeeee........eeee................eeeeeeee.....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:165-264 (gaps) UniProt: 71-264 [INCOMPLETE]                                        Exon 1.3  PDB: B:265-340 UniProt: 265-340                                    Transcript 1
                 3agx B 165 THDLRVSLEEIYSGCTKKMKI------------------LTIEVKKGWKEGTKITFPK----------ADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRTIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI 340
                                   174       184|        -       204       214       | -       234       244       254       264       274       284       294       304       314       324       334      
                                              185                204               222        233                                                                                                           

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DNJB1_HUMAN | P25685)
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: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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0070389    chaperone cofactor-dependent protein refolding    The process of assisting in the restoration of the biological activity of an unfolded or misfolded protein, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0051085    chaperone mediated protein folding requiring cofactor    The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0090084    negative regulation of inclusion body assembly    Any process that decreases the rate, frequency, or extent of inclusion body assembly. Inclusion body assembly is the aggregation, arrangement and bonding together of a set of components to form an inclusion body.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    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:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0006986    response to unfolded protein    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DNJB1_HUMAN | P256851hdj 2qld 3agy 3agz 4wb7

(-) Related Entries Specified in the PDB File

3agy 3agz