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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BINARY COMPLEX OF KRIT1 BOUND TO THE RAP1 GTPASE
 
Authors :  A. R. Gingras
Date :  02 Oct 12  (Deposition) - 10 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ra Binding Motif, Ptb Fold, Gtpase, Gtp, Rap Effector, Rap1, Heg1, Cell-Cell Junctions, Nucleus, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Gingras, W. Puzon-Mclaughlin, M. H. Ginsberg
The Structure Of The Ternary Complex Of Krev Interaction Trapped 1 (Krit1) Bound To Both The Rap1 Gtpase And The Heart Of Glass (Heg1) Cytoplasmic Tail.
J. Biol. Chem. V. 288 23639 2013
PubMed-ID: 23814056  |  Reference-DOI: 10.1074/JBC.M113.462911

(-) Compounds

Molecule 1 - KREV INTERACTION TRAPPED PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLEICS-07
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FERM DOMAIN (UNP RESIDUES 417-736)
    Gene: KRIT1, CCM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: KRIT1, KREV INTERACTION TRAPPED 1, CEREBRAL CAVERNOUS MALFORMATIONS 1 PROTEIN
 
Molecule 2 - RAS-RELATED PROTEIN RAP-1B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTAC
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-167
    Gene: RAP1B, OK/SW-CL.11
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAP1B, GTP-BINDING PROTEIN SMG P21B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2GOL1Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:471 , PHE A:639 , HOH A:934BINDING SITE FOR RESIDUE GOL A 801
2AC2SOFTWARESER B:17 , THR B:35 , GNP B:201 , HOH B:385 , HOH B:386BINDING SITE FOR RESIDUE MG B 200
3AC3SOFTWAREGLY B:13 , VAL B:14 , GLY B:15 , LYS B:16 , SER B:17 , ALA B:18 , PHE B:28 , VAL B:29 , GLU B:30 , TYR B:32 , PRO B:34 , THR B:35 , GLY B:60 , ASN B:116 , LYS B:117 , ASP B:119 , LEU B:120 , SER B:147 , ALA B:148 , LYS B:149 , MG B:200 , HOH B:305 , HOH B:313 , HOH B:384 , HOH B:385 , HOH B:386BINDING SITE FOR RESIDUE GNP B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HDO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HDO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HDO)

(-) Exons   (0, 0)

(no "Exon" information available for 4HDO)

(-) 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:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeeee..hhhhhhhhhhhhh...hhhhhh.eeeeeee..eeee.....hhhhhhhhhhhhhhhhh..hhhhh..eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeee...eeeeee.....eeeeee...eeeee.....eeeeee....eeeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdo A 417 KPYEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKNHKVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQLM 730
                                   426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646||     660       670       680       690       700       710       720       730
                                                                                                                                                                                                                                                                647|                                                                              
                                                                                                                                                                                                                                                                 652                                                                              


Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains d4hdob_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee.....hhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdo B   1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                    10        20        30        40        50        60 ||     74        84        94       104       114       124       134       144       154       164   
                                                                                        62|                                                                                                    
                                                                                         67
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HDO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HDO)

(-) Gene Ontology  (39, 48)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4hdo
    Family and Domain Information: ProDom | SYSTERS
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Access by UniProt ID/Accession number
  KRIT1_HUMAN | O00522
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  RAP1B_HUMAN | P61224
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 Related Entries

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

UniProtKB/Swiss-Prot
        KRIT1_HUMAN | O00522: 3u7d 4dx8 4dxa 4hdq 4jif 4tkn 5d68
        RAP1B_HUMAN | P61224: 3brw 3cf6 4dxa 4hdq 4m8n 4mgi 4mgk 4mgy 4mgz 4mh0 5kho

(-) Related Entries Specified in the PDB File

4hdq KRIT1 FERM DOMAIN + RAP1B + HEG1