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(-) Description

Title :  ANOMALOUS SUBSTRUCTURE OF NBR1PB1
 
Authors :  C. Mueller-Dieckmann, M. S. Weiss
Date :  22 Feb 06  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Anomalous Substructure Of Nbr1Pb1, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Mueller-Dieckmann, S. Panjikar, A. Schmidt, S. Mueller, J. Kuper, A. Geerlof, M. Wilmanns, R. K. Singh, P. A. Tucker, M. S. Weiss
On The Routine Use Of Soft X-Rays In Macromolecular Crystallography. Part Iv. Efficient Determination Of Anomalous Substructures In Biomacromolecules Using Longer X-Ray Wavelengths.
Acta Crystallogr. , Sect. D V. 63 366 2007
PubMed-ID: 17327674  |  Reference-DOI: 10.1107/S0907444906055624

(-) Compounds

Molecule 1 - NEXT TO BRCA1 GENE 1 PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentPB1 DOMAIN
    GeneNBR1,1A13B, KIAA0049, M17S2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEIGHBOR OF BRCA1 GENE 1 PROTEIN, NBR1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:44BINDING SITE FOR RESIDUE CL A 86
2AC2SOFTWAREPRO A:23 , GLU A:24 , THR A:26 , GLN A:61 , TYR A:64 , GLU A:65 , LEU A:68BINDING SITE FOR RESIDUE ACY A 87

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G4S)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:0 -Met A:1

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G4S)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PB1PS51745 PB1 domain profile.NBR1_HUMAN4-85  1A:4-85

(-) Exons   (0, 0)

(no "Exon" information available for 2G4S)

(-) 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:86
 aligned with NBR1_HUMAN | Q14596 from UniProtKB/Swiss-Prot  Length:966

    Alignment length:86
                             1                                                                                    
                             |       9        19        29        39        49        59        69        79      
            NBR1_HUMAN    - -MEPQVTLNVTFKNEIQSFLVSDPENTTWADIEAMVKVSFDLNTIQIKYLDEENEEVSINSQGEYEEALKMAVKQGNQLQMQVHEG 85
               SCOP domains d2g4sa_ A: automated matches                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh...eeeeee.....eeee.hhhhhhhhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PB1  PDB: A:4-85 UniProt: 4-85                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2g4s A  0 AMEPQVTLNVTFKNEIQSFLVSDPENTTWADIEAMVKVSFDLNTIQIKYLDEENEEVSINSQGEYEEALKMAVKQGNQLQMQVHEG 85
                                     9        19        29        39        49        59        69        79      

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G4S)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NBR1_HUMAN | Q14596)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0051019    mitogen-activated protein kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0045668    negative regulation of osteoblast differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0030500    regulation of bone mineralization    Any process that modulates the frequency, rate or extent of bone mineralization.
    GO:0032872    regulation of stress-activated MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
cellular component
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    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: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: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: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:0000407    pre-autophagosomal structure    Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NBR1_HUMAN | Q145961wj6 2bkf 2cp8 2l8j 2mgw 2mj5 4ole

(-) Related Entries Specified in the PDB File

2g4h 2g4i 2g4j 2g4k 2g4l 2g4m 2g4n 2g4o 2g4p 2g4q 2g4r 2g4t 2g4u 2g4v 2g4w 2g4x 2g4y 2g4z 2g51 2g52 2g55