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(-) Description

Title :  YEAST NBP2P SH3 DOMAIN IN COMPLEX WITH A PEPTIDE FROM STE20P
 
Authors :  M. Gorelik, A. R. Davidson
Date :  07 May 11  (Deposition) - 01 Feb 12  (Release) - 11 Apr 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Adaptor, Transferase, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Gorelik, A. R. Davidson
Distinct Peptide Binding Specificities Of Src Homology 3 (Sh3) Protein Domains Can Be Determined By Modulation Of Local Energetics Across The Binding Interface.
J. Biol. Chem. V. 287 9168 2012
PubMed-ID: 22277653  |  Reference-DOI: 10.1074/JBC.M111.330753

(-) Compounds

Molecule 1 - NAP1-BINDING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET21
    FragmentSH3 DOMAIN RESIDUES 110-172
    GeneNBP2, YDR162C
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 2 - SERINE/THREONINE-PROTEIN KINASE STE20
    ChainsB
    EC Number2.7.11.1
    EngineeredYES
    FragmentSEQUENCE DATABASE RESIDUES 468-483
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE S288C
    Organism Taxid559292
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LCS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NBP2_YEAST110-171  1A:-2-60
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.NBP2_YEAST110-171  1A:-2-60

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR162C1YDR162C.1IV:781098-780388711NBP2_YEAST1-2362361A:-4-63 (gaps)94

(-) 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:67
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:94
                                    95       105       115       125       135       145       155       165       175    
           NBP2_YEAST    86 MVSDSSNGEDTYNKRQSITLPDDYIVNQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQPEDGENEVE 179
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..----------------------...eeeee..................eeeeeeee...eeeee......eeeee...eee...-----... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SH3  PDB: A:-2-60 UniProt: 110-171                            -------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:-4-63 (gaps) UniProt: 1-236 [INCOMPLETE]                                      Transcript 1
                 2lcs A  -4 MA----------------------IVNQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQP-----ELE  63
                             |       -         -    |||  4        14        24        34        44        54     |   - |  
                             |                     -2||                                                         60    61  
                            -3                      -1|                                                                   
                                                      1                                                                   

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with STE20_YEAST | Q03497 from UniProtKB/Swiss-Prot  Length:939

    Alignment length:16
                                   477      
          STE20_YEAST   468 GKFIPSRPAPKPPSSA 483
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2lcs B  -9 GKFIPSRPAPKPPSSA   6
                                     0      

   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  (0, 0)

(no "SCOP Domain" information available for 2LCS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 44)

NMR Structure(hide GO term definitions)
Chain A   (NBP2_YEAST | Q12163)
molecular function
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    GO:0006972    hyperosmotic response    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 detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
    GO:0000200    inactivation of MAPK activity involved in cell wall organization or biogenesis    Any process that terminates the activity of the active enzyme MAP kinase in the context of cell wall organization or biogenesis.
    GO:0000173    inactivation of MAPK activity involved in osmosensory signaling pathway    Any process that terminates the activity of the active enzyme MAP kinase during osmolarity sensing.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B   (STE20_YEAST | Q03497)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008349    MAP kinase kinase kinase kinase activity    Catalysis of the phosphorylation of serine and threonine residues in a mitogen-activated protein kinase kinase kinase (MAPKKK), resulting in activation of MAPKKK. MAPKKK signaling pathways relay, amplify and integrate signals from the plasma membrane to the nucleus in response to a diverse range of extracellular stimuli.
    GO:0044025    histone kinase activity (H2B-S14 specific)    Catalysis of the transfer of a phosphate group to the serine-14 or an equivalent residue of the N-terminal tail of histone H2B.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0000185    activation of MAPKKK activity    Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK).
    GO:0007121    bipolar cellular bud site selection    The process of defining subsequent sites of bud emergence such that budding takes place at alternating poles of a budding cell.
    GO:0007118    budding cell apical bud growth    Growth at the tip of a bud, in a cell that reproduces by budding.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0034605    cellular response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0043991    histone H2B-S14 phosphorylation    The modification of histone H2B by the addition of an phosphate group to a serine residue at position 14 of the histone.
    GO:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1990872    negative regulation of sterol import by negative regulation of transcription from RNA polymerase II promoter    Any process that decreases the frequency, rate or extent of sterol import, by down regulation of transcription from an RNA polymerase II promoter.
    GO:0007232    osmosensory signaling pathway via Sho1 osmosensor    A series of molecular signals generated in response to osmotic change, as mediated through a Sho1 osmosensor system.
    GO:0000750    pheromone-dependent signal transduction involved in conjugation with cellular fusion    A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007124    pseudohyphal growth    A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.
    GO:0007096    regulation of exit from mitosis    Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.
    GO:0019236    response to pheromone    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 pheromone stimulus.
    GO:0001402    signal transduction involved in filamentous growth    Relaying of environmental signals promoting filamentous growth.
    GO:0035376    sterol import    The directed movement of a sterol into a cell or organelle. Sterols are steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    GO:0034063    stress granule assembly    The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
    GO:0000011    vacuole inheritance    The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000131    incipient cellular bud site    The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
    GO:0043332    mating projection tip    The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
    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
        NBP2_YEAST | Q121631yn8
        STE20_YEAST | Q034972kym 2rqw

(-) Related Entries Specified in the PDB File

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