Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RAS-BRY2RBD COMPLEX
 
Authors :  K. Scheffzek, P. Gruenewald, S. Wohlgemuth, W. Kabsch, H. Tu, M. Wigler, A. Wittinghofer, C. Herrmann
Date :  25 Oct 01  (Deposition) - 13 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signal Transduction, Cancer, Gtpase, Ubiquitin Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Scheffzek, P. Grunewald, S. Wohlgemuth, W. Kabsch, H. Tu, M. Wigler, A. Wittinghofer, C. Herrmann
The Ras-Byr2Rbd Complex: Structural Basis For Ras Effector Recognition In Yeast.
Structure V. 9 1043 2001
PubMed-ID: 11709168  |  Reference-DOI: 10.1016/S0969-2126(01)00674-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSFORMING PROTEIN P21/H-RAS-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainCK600K
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentGTP-BINDING/CATALYTIC DOMAIN, RESIDUES 1-166
    GeneHRAS OR HRAS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - PROTEIN KINASE BYR2
    ChainsB
    EC Number2.7.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRAS BINDING DOMAIN (RBD), RESIDUES 71-180
    GeneBYR2 OR STE8 OR SPBC1D7.05
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:16 , SER A:17 , THR A:35 , ASP A:57 , THR A:58 , GNP A:167BINDING SITE FOR RESIDUE MG A 168
2AC2SOFTWAREGLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , ASP A:30 , GLU A:31 , TYR A:32 , PRO A:34 , THR A:35 , GLY A:60 , ASN A:116 , LYS A:117 , ASP A:119 , LEU A:120 , SER A:145 , ALA A:146 , LYS A:147 , MG A:168BINDING SITE FOR RESIDUE GNP A 167

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K8R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (18, 18)

Asymmetric/Biological Unit (18, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_026106G12ARASH_HUMANDisease (CSTLO)104894230AG12A
02UniProtVAR_045975G12CRASH_HUMANDisease (CSTLO)104894229AG12C
03UniProtVAR_068816G12DRASH_HUMANDisease (CSTLO)104894230AG12D
04UniProtVAR_045976G12ERASH_HUMANDisease (CSTLO)  ---AG12E
05UniProtVAR_006837G12SRASH_HUMANDisease (CSTLO)104894229AG12S
06UniProtVAR_006836G12VRASH_HUMANDisease (CSTLO)104894230AG12V
07UniProtVAR_026107G13CRASH_HUMANDisease (CSTLO)104894228AG13C
08UniProtVAR_026108G13DRASH_HUMANDisease (CSTLO)104894226AG13D
09UniProtVAR_068817G13RRASH_HUMANDisease (SFM)104894228AG13R
10UniProtVAR_045977Q22KRASH_HUMANDisease (CMEMS)121917757AQ22K
11UniProtVAR_045978T58IRASH_HUMANDisease (CSTLO)121917758AT58I
12UniProtVAR_045979Q61KRASH_HUMANDisease (NMTC2)28933406AQ61K
13UniProtVAR_006838Q61LRASH_HUMANUnclassified121913233AQ61L
14UniProtVAR_045980E63KRASH_HUMANDisease (CMEMS)121917756AE63K
15UniProtVAR_078259S89CRASH_HUMANUnclassified755322824AS89C
16UniProtVAR_045981K117RRASH_HUMANDisease (CSTLO)104894227AK117R
17UniProtVAR_045982A146TRASH_HUMANDisease (CSTLO)104894231AA146T
18UniProtVAR_045983A146VRASH_HUMANDisease (CSTLO)121917759AA146V

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASPS51421 small GTPase Ras family profile.RASH_HUMAN1-188  1A:1-166

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003975963ENSE00001529352chr11:535339-53525783RASH_HUMAN-00--
1.5bENST000003975965bENSE00002189675chr11:534375-534212164RASH_HUMAN1-37371A:1-3737
1.6cENST000003975966cENSE00001728710chr11:533944-533766179RASH_HUMAN38-97601A:38-9760
1.7aENST000003975967aENSE00001206466chr11:533612-533453160RASH_HUMAN97-150541A:97-15054
1.9dENST000003975969dENSE00001628271chr11:532755-532242514RASH_HUMAN151-189391A:151-16616

(-) 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:166
 aligned with RASH_HUMAN | P01112 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      
           RASH_HUMAN     1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH 166
               SCOP domains d1k8ra_ A: cH-p21 Ras protein                                                                                                                                          SCOP domains
               CATH domains 1k8rA00 A:1-166 P-loop containing nucleotide triphosphate hydrolases                                                                                                   CATH domains
               Pfam domains ----Ras-1k8rA01 A:5-165                                                                                                                                              - Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhh............eeeeeeeee..eeeeeeeee...hhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----------AC--------K-----------------------------------I--K-K-------------------------C---------------------------R----------------------------T-------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------CD-----------------------------------------------L------------------------------------------------------------------------------------V-------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------DR--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -----------E---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
             SAPs(SNPs) (5) -----------S---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (5)
             SAPs(SNPs) (6) -----------V---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (6)
                    PROSITE RAS  PDB: A:1-166 UniProt: 1-188                                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.5b  PDB: A:1-37 UniProt: 1-37 Exon 1.6c  PDB: A:38-97 UniProt: 38-97                      -----------------------------------------------------Exon 1.9d        Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------Exon 1.7a  PDB: A:97-150 UniProt: 97-150              ---------------- Transcript 1 (2)
                 1k8r A   1 MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with BYR2_SCHPO | P28829 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:95
                                    80        90       100       110       120       130       140       150       160     
           BYR2_SCHPO    71 CILRFIACNGQTRAVQSRGDYQKTLAIALKKFSLEDASKFIVCVSQSSRIKLITEEEFKQICFNSSSPERDRLIIVPKEKPCPSFEDLRRSWEIE 165
               SCOP domains d1k8rb_ B: Protein kinase byr2                                                                  SCOP domains
               CATH domains 1k8rB00 B:71-165 Phosphatidylinositol 3-kinase Catalytic              Subunit; Chain A, domain  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee...hhhhhhhhhhhhhh......eeeeee....eee....-------------...eeeee......hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 1k8r B  71 CILRFIACNGQTRAVQSRGDYQKTLAIALKKFSLEDASKFIVCVSQSSRIKLITEE-------------RDRLIIVPKEKPCPSFEDLRRSWEIE 165
                                    80        90       100       110       120     |   -       140       150       160     
                                                                                 126           140                         

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: Ras (176)

(-) Gene Ontology  (87, 91)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RASH_HUMAN | P01112)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + 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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0042088    T-helper 1 type immune response    An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007569    cell aging    An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0042832    defense response to protozoan    Reactions triggered in response to the presence of a protozoan that act to protect the cell or organism.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0097193    intrinsic apoptotic signaling pathway    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:0034260    negative regulation of GTPase activity    Any process that stops or reduces the rate of GTP hydrolysis by a GTPase.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0046579    positive regulation of Ras protein signal transduction    Any process that activates or increases the frequency, rate or extent of Ras protein signal transduction.
    GO:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases 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:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:2000630    positive regulation of miRNA metabolic process    Any process that activates or increases the frequency, rate or extent of miRNA metabolic process.
    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:1900029    positive regulation of ruffle assembly    Any process that activates or increases the frequency, rate or extent of ruffle assembly.
    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:0090303    positive regulation of wound healing    Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
    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:0048169    regulation of long-term neuronal synaptic plasticity    A process that modulates long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    GO:0035176    social behavior    Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B   (BYR2_SCHPO | P28829)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004709    MAP kinase kinase kinase activity    Catalysis of the phosphorylation and activation of a MAP kinase kinase; each MAP kinase kinase can be phosphorylated by any of several MAP kinase kinase kinases.
    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: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:1903695    MAPK cascade involved in ascospore formation    Any MAPK cascade that is involved in ascospore formation.
    GO:0071507    MAPK cascade involved in conjugation with cellular fusion    A MAPK cascade that contributes to conjugation with cellular fusion.
    GO:0000186    activation of MAPKK activity    The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK).
    GO:0000185    activation of MAPKKK activity    Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK).
    GO:0000746    conjugation    The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
    GO:0031142    induction of conjugation upon nitrogen starvation    The process in which a cell initiates conjugation with cellular fusion upon nitrogen starvation.
    GO:0010514    induction of conjugation with cellular fusion    The process in which a cell initiates conjugation with cellular fusion. Conjugation with cellular fusion is the process that results in the union of cellular and genetic information from compatible mating types.
    GO:0000751    mitotic cell cycle G1 arrest in response to pheromone    The cell cycle regulatory process in which the mitotic cell cycle is halted during G1 as a result of a pheromone stimulus. An example of this process is found in Saccharomyces cerevisiae.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032005    signal transduction involved in conjugation with cellular fusion    The series of molecular signals that bring about the relay, amplification or dampening of a signal generated in response to a cue, such as starvation or pheromone exposure, in organisms that undergo conjugation with cellular fusion.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0000935    barrier septum    A septum which spans a cell and does not allow exchange of organelles or cytoplasm between compartments.
    GO:0032153    cell division site    The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
    GO:0051286    cell tip    The region at the end of the longest axis of a cylindrical or elongated cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GNP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k8r)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1k8r
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BYR2_SCHPO | P28829
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  RASH_HUMAN | P01112
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  163200
    Disease InformationOMIM
  188470
    Disease InformationOMIM
  218040
    Disease InformationOMIM
 
Access by GenAge ID
  0038
    Age Related InformationGenAge
  0154
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BYR2_SCHPO | P28829
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RASH_HUMAN | P01112
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BYR2_SCHPO | P288291i35
        RASH_HUMAN | P01112121p 1aa9 1agp 1bkd 1clu 1crp 1crq 1crr 1ctq 1gnp 1gnq 1gnr 1he8 1iaq 1ioz 1jah 1jai 1lf0 1lf5 1lfd 1nvu 1nvv 1nvw 1nvx 1p2s 1p2t 1p2u 1p2v 1plj 1plk 1pll 1q21 1qra 1rvd 1wq1 1xcm 1xd2 1xj0 1zvq 1zw6 221p 2c5l 2ce2 2cl0 2cl6 2cl7 2clc 2cld 2evw 2gdp 2lcf 2lwi 2n42 2n46 2q21 2quz 2rga 2rgb 2rgc 2rgd 2rge 2rgg 2uzi 2vh5 2x1v 3ddc 3i3s 3k8y 3k9l 3k9n 3kkm 3kkn 3kud 3l8y 3l8z 3lbh 3lbi 3lbn 3lo5 3oiu 3oiv 3oiw 3rry 3rrz 3rs0 3rs2 3rs3 3rs4 3rs5 3rs7 3rsl 3rso 3tgp 421p 4dlr 4dls 4dlt 4dlu 4dlv 4dlw 4dlx 4dly 4dlz 4dst 4dsu 4efl 4efm 4efn 4g0n 4g3x 4k81 4l9s 4l9w 4nyi 4nyj 4nym 4q21 4rsg 4uru 4urv 4urw 4urx 4ury 4urz 4us0 4us1 4us2 4xvq 4xvr 521p 5b2z 5b30 5e95 5p21 621p 6q21 721p 821p

(-) Related Entries Specified in the PDB File

1c1y CRYSTAL STRUCTURE OF RAP. GMPPNP IN COMPLEX WITH THE RAS- BINDING-DOMAIN OF C-RAF1 KINASE (RAFRBD).
1he8 RAS G12V - 3-KINASE COMPLEX
1lfd CRYSTAL STRUCTURE OF THE ACTIVE RAS PROTEIN COMPLEXED WITH THE RAS-INTERACTING DOMAIN OF RALGDS