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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN 70KDA HEAT SHOCK PROTEIN 2 (HSP70-2) ATPASE DOMAIN IN COMPLEX WITH ADP AND INORGANIC PHOSPHATE
 
Authors :  M. Wisniewska, T. Karlberg, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammar A. Johansson, I. Johansson, T. Kotenyova, A. Kotzsch, T. K. Nielsen, P. Nordlund, T. Nyman, M. Moche, C. Persson, A. K. Roos, J. Sagemark, P. M. I. Siponen, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weig M. Welin, H. Schueler, Structural Genomics Consortium (Sgc)
Date :  30 Jun 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Adp Complex, Atp-Binding, Chaperone, Nucleotide-Binding, Phosphoprotein, Stress Response, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Wisniewska, T. Karlberg, L. Lehtio, I. Johansson, T. Kotenyova, M. Moche, H. Schueler
Crystal Structures Of The Atpase Domains Of Four Human Hsp7 Isoforms: Hspa1L/Hsp70-Hom, Hspa2/Hsp70-2, Hspa6/Hsp70B', And Hspa5/Bip/Grp78
Plos One V. 5 E8625 2010
PubMed-ID: 20072699  |  Reference-DOI: 10.1371/JOURNAL.PONE.0008625

(-) Compounds

Molecule 1 - HEAT SHOCK-RELATED 70 KDA PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)R3PRARE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentATP-ASE DOMAIN, RESIDUES 6-386
    GeneHSPA2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEAT SHOCK 70 KDA PROTEIN 2, HSP70-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , THR A:14 , LYS A:72 , PRO A:148 , GLU A:176 , THR A:207 , ADP A:388 , MG A:389 , HOH A:418 , HOH A:436 , HOH A:460 , HOH A:462 , HOH A:487 , HOH A:524BINDING SITE FOR RESIDUE PO4 A 387
2AC2SOFTWARETHR A:14 , THR A:15 , TYR A:16 , GLY A:204 , GLY A:205 , GLY A:233 , GLU A:271 , LYS A:274 , ARG A:275 , SER A:278 , GLY A:341 , GLY A:342 , SER A:343 , ARG A:345 , ASP A:369 , PO4 A:387 , MG A:389 , HOH A:391 , HOH A:411 , HOH A:418 , HOH A:432 , HOH A:453 , HOH A:460 , HOH A:462 , HOH A:505 , HOH A:533 , HOH A:656 , HOH A:696 , HOH A:721BINDING SITE FOR RESIDUE ADP A 388
3AC3SOFTWAREPO4 A:387 , ADP A:388 , HOH A:460 , HOH A:462 , HOH A:505 , HOH A:524BINDING SITE FOR RESIDUE MG A 389
4AC4SOFTWARETHR A:14 , LYS A:72 , ARG A:73 , ARG A:77 , TYR A:150 , PHE A:151 , GLN A:155 , THR A:207 , THR A:229 , HOH A:498BINDING SITE FOR RESIDUE GOL A 390

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032706C191SHSP72_HUMANPolymorphism45456191AC191S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP70_1PS00297 Heat shock hsp70 proteins family signature 1.HSP72_HUMAN10-17  1A:10-17
2HSP70_2PS00329 Heat shock hsp70 proteins family signature 2.HSP72_HUMAN200-213  1A:200-213
3HSP70_3PS01036 Heat shock hsp70 proteins family signature 3.HSP72_HUMAN337-351  1A:337-351

(-) Exons   (0, 0)

(no "Exon" information available for 3I33)

(-) 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:380
 aligned with HSP72_HUMAN | P54652 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:380
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384
          HSP72_HUMAN     5 GPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAKRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGETKTFFPEEISSMVLTKMKEIAEAYLGGKVHSAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILI 384
               SCOP domains d3i33a1 A:5-189 automated matches                                                                                                                                                        d3i33a2 A:190-384 automated matches                                                                                                                                                                 SCOP domains
               CATH domains 3i33A01 A:5-68,A:124-188,A:364-384                              3i33A02 A:69-123  [code=3.30.30.30, no name defined]   3i33A01 A:5-68,A:124-188,A:364-384                               3i33A03 A:189-231,A:316-363                3i33A04 A:232-315 Actin; Chain A, domain 4                                          3i33A03 A:189-231,A:316-363                     3i33A01               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeeeee..eeee.........ee..eee....eeehhhhhhh.......ee.hhhhh......hhhhhhhhh....eeeee..eeeeeeee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhh............eeeeeee....eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HSP70_1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HSP70_2       ---------------------------------------------------------------------------------------------------------------------------HSP70_3        --------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i33 A   5 MPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAKRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGETKTFFPEEISSMVLTKMKEIAEAYLGGKVHSAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILI 384
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384

   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/Biological Unit

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I33)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HSP72_HUMAN | P54652)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0051861    glycolipid binding    Interacting selectively and non-covalently with a glycolipid, any compound containing one or more monosaccharide residues bound by a glycosidic linkage to a hydrophobic group such as an acylglycerol, a sphingoid, a ceramide (N-acylsphingoid) or a prenyl phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007141    male meiosis I    A cell cycle process comprising the steps by which a cell progresses through male meiosis I, the first meiotic division in the male germline.
    GO:0007140    male meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
    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:1901896    positive regulation of calcium-transporting ATPase activity    Any process that activates or increases the frequency, rate or extent of calcium-transporting ATPase activity.
    GO:0031662    positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle    Any process that activates or increases the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity involved in the G2/M transition of the cell cycle.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0009409    response to cold    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 a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
    GO:0009408    response to heat    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 a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    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.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0070194    synaptonemal complex disassembly    The controlled breakdown of a synaptonemal complex.
cellular component
    GO:0036128    CatSper complex    A sperm-specific voltage-gated calcium channel that controls the intracellular calcium ion concentration and, thereby, the swimming behavior of sperm. Consists of a heteromeric tetramer surrounding a calcium ion- selective pore. May also contain additional auxiliary subunits.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0001673    male germ cell nucleus    The nucleus of a male germ cell, a reproductive cell in males.
    GO:0072687    meiotic spindle    A spindle that forms as part of meiosis. Several proteins, such as budding yeast Spo21p, fission yeast Spo2 and Spo13, and C. elegans mei-1, localize specifically to the meiotic spindle and are absent from the mitotic spindle.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0000795    synaptonemal complex    A proteinaceous scaffold found between homologous chromosomes during meiosis. It consists of 2 lateral elements and a central element, all running parallel to each other. Transverse filaments connect the lateral elements to the central element.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HSP72_HUMAN | P546524fsv 5fpd 5fpe 5fpm 5fpn

(-) Related Entries Specified in the PDB File

3fe1 THE HUMAN HEAT SHOCK 70KDA PROTEIN 6 (HSP70B') ATP-ASE DOMAIN IN COMPLEX WITH ADP
3gdq THE HUMAN 70KDA HEAT SHOCK PROTEIN 1-LIKE ATPASE DOMAIN IN COMPLEX WITH ADP AND INORGANIC PHOSPHATE