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Co-crystal structure of Rap1 in complex with KRIT1
Biology and Chemistry Report
4DXA
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN BINDING
    Text GTPase, FERM, Protein-protein interaction, GTP binding, Cytoplasmic, PROTEIN BINDING

    Polymeric Molecules

    Chain A
    Description Ras-related protein Rap-1b 
    Mutation G12V 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 19206.9 
    Source Method genetically manipulated  
    Entity Name GTP-binding protein smg p21B 
    Chain B
    Description Krev interaction trapped protein 1 
    Fragment FERM domain 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 37372.6 
    Source Method genetically manipulated  
    Entity Name Krev interaction trapped 1, Cerebral cavernous malformations 1 protein 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GSP  5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE  C10 H16 N5 O13 P3 S   539.25  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A RAP1B_HUMAN B2R5Z2     
    B KRIT1_HUMAN A6NNU0     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    3.6.5.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6112   Energy Reserve Metabolic Process  The Chemical Reactions and Pathways by Which a Cell Derives Energy From Stored Compounds Such As Fats or Glycogen. 
    6184   GTP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    7165   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. 
    7264   Small Gtpase Mediated Signal Transduction  Any Series of Molecular Signals in Which a Small Monomeric Gtpase Relays One or More of the Signals. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    8283   Cell Proliferation  The Multiplication or Reproduction of Cells Resulting in the Expansion of a Cell Population. 
    15031   Protein Transport  The Directed Movement of Proteins Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    30168   Platelet Activation  A Series of Progressive Overlapping Events Triggered by Exposure of the Platelets to Subendothelial Tissue. These Events Include Shape Change Adhesiveness Aggregation and Release Reactions. When Carried Through to Completion These Events Lead to the Formation of a Stable Hemostatic Plug. 
    32486   Rap Protein Signal Transduction  A Series of Molecular Signals Within the Cell That Are Mediated by a Member of the Rap Family of Proteins Switching to a GTP Bound Active State. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    45955   Negative Regulation of Calcium Ion Dependent Exocytosis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Calcium Ion Dependent Exocytosis. 
    50796   Regulation of Insulin Secretion  Any Process That Modulates the Frequency Rate or Extent of the Regulated Release of Insulin. 
    61028   Establishment of Endothelial Barrier  The Establishment of a Barrier Between Endothelial Cell Layers Such As Those in the Brain Lung or Intestine to Exert Specific and Selective Control Over the Passage of Water and Solutes Thus Allowing Formation and Maintenance of Compartments That Differ in Fluid and Solute Composition. 
    70374   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. 
    71320   Cellular Response to Camp  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 Camp (cyclic AMP Adenosine 3' 5' Cyclophosphate) Stimulus. 
    1901888   Regulation of Cell Junction Assembly  Any Process That Modulates the Frequency Rate or Extent of Cell Junction Assembly. 
    2000114   Regulation of Establishment of Cell Polarity  Any Process That Modulates the Frequency Rate or Extent of Establishment of Cell Polarity. 
    2000301   Negative Regulation of Synaptic Vesicle Exocytosis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Synaptic Vesicle Exocytosis. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5811   Lipid Particle  An Intracellular Non Membrane Bounded Organelle Comprising a Matrix of Coalesced Lipids Surrounded by a Phospholipid Monolayer. May Include Associated Proteins. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    5911   Cell Cell Junction  A Cell Junction That Forms a Connection Between Two Cells; Excludes Direct Cytoplasmic Junctions Such As Ring Canals. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    30054   Cell Junction  A Cellular Component That Forms a Specialized Region of Connection Between Two Cells or Between a Cell and the Extracellular Matrix. At a Cell Junction Anchoring Proteins Extend Through the Plasma Membrane to Link Cytoskeletal Proteins in One Cell to Cytoskeletal Proteins in Neighboring Cells or to Proteins in the Extracellular Matrix. 
    45121   Membrane Raft  Any of the Small (10 200 Nm) Heterogeneous Highly Dynamic Sterol and Sphingolipid Enriched Membrane Domains That Compartmentalize Cellular Processes. Small Rafts Can Sometimes Be Stabilized to Form Larger Platforms Through Protein Protein and Protein Lipid Interactions. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    166   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. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5515   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). 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    19003   GDP Binding  Interacting Selectively and Non Covalently with GDP Guanosine 5' Diphosphate. 
    32403   Protein Complex Binding  Interacting Selectively and Non Covalently with Any Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    Chain B
    GO ID   Ontology GO Term Definition
    5856   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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ccm1, krev interaction trapped protein 1 (krit1), krit1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pGEX 6p-1


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ok/sw-cl.11, rap1b, ras-related protein rap-1b (rap1b)
    Host Scientific Name Escherichia coli  
    Host Strain Rosetta
    Host Vector Type Plasmid
    Host Plasmid Name modified pET-32


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    7 7q21.2 889     KRIT1, ankyrin repeat containing KRIT1    
    12 12q14 5908     RAP1B, member of RAS oncogene family RAP1B    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs139690878 LS-SNP   dbSNP   B 422 V - > I Beta Ladder 14% (Intermediate) 7 91852283
    rs138326046 LS-SNP   dbSNP   B 427 M - > T Turn 13% (Intermediate) 7 91852267
    rs201272513 LS-SNP   dbSNP   B 452 R - > H Bend 21% (Intermediate) 7 91852192
    rs190329675 LS-SNP   dbSNP   B 460 Y - > C 3/10 Helix 10% (Intermediate) 7 91852168
    rs141514714 LS-SNP   dbSNP   B 462 T - > A Beta Ladder 7% (Buried) 7 91852163
    rs148355366 LS-SNP   dbSNP   B 482 Q - > H Helix 21% (Intermediate) 7 91851333
    rs145845538 LS-SNP   dbSNP   B 485 R - > H Helix 52% (Exposed) 7 91851325
    rs142071709 LS-SNP   dbSNP   B 518 V - > A Helix 46% (Exposed) 7 91851226
    rs149975731 LS-SNP   dbSNP   B 522 I - > V Coil 2% (Buried) 7 91844091
    rs137861350 LS-SNP   dbSNP   B 547 P - > A Coil 72% (Exposed) 7 91844016
    rs146927768 LS-SNP   dbSNP   B 561 I - > V Helix 11% (Intermediate) 7 91843974
    rs140810405 LS-SNP   dbSNP   B 610 T - > I Coil 91% (Exposed) 7 91842705
    rs35311859 LS-SNP   dbSNP   B 613 G - > D Coil 154% (Exposed) 7 91842696
    rs202116909 LS-SNP   dbSNP   B 620 H - > R Helix 35% (Intermediate) 7 91842675
    rs143644029 LS-SNP   dbSNP   B 623 R - > H Helix 26% (Intermediate) 7 91842666
    rs201527319 LS-SNP   dbSNP   B 645 F - > L Beta Ladder 65% (Exposed) 7 91842601
    rs202120786 LS-SNP   dbSNP   B 663 N - > S Coil 0% (Buried) 7 91842546
    rs201207694 LS-SNP   dbSNP   B 672 M - > V Turn 27% (Intermediate) 7 91842520
    rs138763545 LS-SNP   dbSNP   B 682 K - > Q Beta Ladder 47% (Exposed) 7 91830719
    rs140875641 LS-SNP   dbSNP   B 702 M - > V Bend 43% (Exposed) 7 91830659
    rs140952803 LS-SNP   dbSNP   B 718 V - > M Helix 0% (Buried) 7 91830109