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(-) Description

Title :  NMR STRUCTURE OF THE UBIQUITIN ASSOCIATED (UBA) DOMAIN OF P62 (SQSTM1) IN COMPLEX WITH UBIQUITIN. RDC REFINED
 
Authors :  J. E. Long, R. Layfield, M. S. Searle
Date :  07 Dec 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Ubiquitin Binding, Ubiquitin Associated Domain, Helical Bundle, Three Helices, Alternative Splicing, Apoptosis, Cytoplasm, Differentiation, Disease Mutation, Endosome, Immune Response, Metal-Binding, Nucleus, Phosphoprotein, Polymorphism, Zinc, Zinc-Finger, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Long, T. R. Gallagher, J. R. Cavey, P. W. Sheppard, S. H. Ralston, R. Layfield, M. S. Searle
Ubiquitin Recognition By The Ubiquitin-Associated Domain Of P62 Involves A Novel Conformational Switch
J. Biol. Chem. V. 283 5427 2008
PubMed-ID: 18083707  |  Reference-DOI: 10.1074/JBC.M704973200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UBIQUITIN-BINDING PROTEIN P62
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21
    Expression System Taxid469008
    Expression System Variant(DE3)
    Expression System VectorPGEX-4T-1
    Expression System Vector TypeVECTOR
    FragmentUBA DOMAIN
    GeneSQSTM1, ORCA, OSIL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSEQUESTOSOME-1, PHOSPHOTYROSINE-INDEPENDENT LIGAND FOR THE LCK SH2 DOMAIN OF 62 KDA, EBI3-ASSOCIATED PROTEIN OF 60 KDA, P60, EBIAP

 Structural Features

(-) Chains, Units

  
NMR Structure (21x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2JY8)

(-) Sites  (0, 0)

(no "Site" information available for 2JY8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JY8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JY8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

NMR Structure (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023592P387LSQSTM_HUMANDisease (PDB3)776749939AP3L
2UniProtVAR_023593P392LSQSTM_HUMANDisease (PDB3)104893941AP8L
3UniProtVAR_023594S399PSQSTM_HUMANDisease (PDB3)  ---AS15P
4UniProtVAR_023595M404TSQSTM_HUMANDisease (PDB3)  ---AM20T
5UniProtVAR_023596M404VSQSTM_HUMANDisease (PDB3)771966860AM20V
6UniProtVAR_023597G411SSQSTM_HUMANDisease (PDB3)143511494AG27S
7UniProtVAR_023598G425RSQSTM_HUMANDisease (PDB3)757212984AG41R
8UniProtVAR_073936T430PSQSTM_HUMANDisease (FTDALS3)770118706AT46P

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UBAPS50030 Ubiquitin-associated domain (UBA) profile.SQSTM_HUMAN389-434  1A:5-50

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.8aENST000003898058aENSE00001591239chr5:179247759-179248141383SQSTM_HUMAN1-69690--
1.10cENST0000038980510cENSE00001694947chr5:179249958-17925005396SQSTM_HUMAN69-101330--
1.11gENST0000038980511gENSE00001055964chr5:179250858-179251087230SQSTM_HUMAN101-177770--
1.12dENST0000038980512dENSE00002170029chr5:179251182-179251323142SQSTM_HUMAN178-225480--
1.13ENST0000038980513ENSE00002192724chr5:179252146-17925222681SQSTM_HUMAN225-252280--
1.14bENST0000038980514bENSE00001601839chr5:179260032-179260246215SQSTM_HUMAN252-323720--
1.15ENST0000038980515ENSE00001648470chr5:179260587-179260782196SQSTM_HUMAN324-389661A:1-5 (gaps)17
1.16cENST0000038980516cENSE00001506956chr5:179263436-1792650781643SQSTM_HUMAN389-440521A:5-5248

(-) 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:52
 aligned with SQSTM_HUMAN | Q13501 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:64
                                   382       392       402       412       422       432    
          SQSTM_HUMAN   373 GPTGLKEAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKH 436
               SCOP domains d2            jy8a_ A: Sequestosome 1 (Sqstm1)                   SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------....hhhhhhhhhhh.........hhhhhhhhhhh.hhhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------L----L------P----T------S-------------R----P------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------V-------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------UBA  PDB: A:5-50 UniProt: 389-434             -- PROSITE
           Transcript 1 (1) Exon 1.15        ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.16c  PDB: A:5-52 UniProt: 389-440         Transcript 1 (2)
                 2jy8 A   1 GS------------PPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKH  52
                             |       -    |    8        18        28        38        48    
                             2            3                                                 

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JY8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JY8)

(-) Gene Ontology  (56, 56)

NMR Structure(hide GO term definitions)
Chain A   (SQSTM_HUMAN | Q13501)
molecular function
    GO:0070530    K63-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein.
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0000422    autophagy of mitochondrion    The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
    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:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0016239    positive regulation of macroautophagy    Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0051291    protein heterooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043122    regulation of I-kappaB kinase/NF-kappaB signaling    Any process that modulates I-kappaB kinase/NF-kappaB signaling.
    GO:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    GO:0010821    regulation of mitochondrion organization    Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a mitochondrion.
    GO:0061635    regulation of protein complex stability    Any process that affects the structure and integrity of a protein complex by altering the likelihood of its assembly or disassembly.
    GO:0006950    response to stress    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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0000932    P-body    A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0016235    aggresome    An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
    GO:0044753    amphisome    Intermediate organelles formed during macroautophagy through the fusion between autophagosomes and endosomes.
    GO:0044754    autolysosome    A type of secondary lysosome in which a primary lysosome has fused with the outer membrane of an autophagosome. It is involved in the second step of autophagy in which it degrades contents with acidic lysosomal hydrolases.
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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: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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    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:0016234    inclusion body    A discrete intracellular part formed of aggregated molecules such as proteins or other biopolymers.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    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.
    GO:0000407    pre-autophagosomal structure    Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
    GO:0097225    sperm midpiece    The highly organized segment of the sperm flagellum which begins at the connecting piece and is characterized by the presence of 9 outer dense fibers (ODFs) that lie outside each of the 9 outer axonemal microtubule doublets and by a sheath of mitochondria that encloses the ODFs and the axoneme; the midpiece terminates about one-fourth of the way down the sperm flagellum at the annulus, which marks the beginning of the principal piece.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SQSTM_HUMAN | Q135011q02 2jy7 2k0b 2knv 4mjs 4uf8 4uf9

(-) Related Entries Specified in the PDB File

2jy7 RELATED ID: 15592 RELATED DB: BMRB