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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
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    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. 
    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. 
    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. 
    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. 


     
  •   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