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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF KRIT1 BOUND TO BOTH THE RAP1 GTPASE AND THE HEART OF GLASS (HEG1) CYTOPLASMIC TAIL
 
Authors :  A. R. Gingras
Date :  02 Oct 12  (Deposition) - 10 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ra Binding Motif, Gtpase, Heg1 Cytoplasmic Tail, Ptd Domain, Rap1 Effector, Transmembrane Protein, Rap1, Heg1, Cell-Cell Junctions, Plasma Membrane, 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
 
Molecule 3 - PROTEIN HEG HOMOLOG 1
    Chains: C
    Engineered: YES
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 1356-1381)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEG1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

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
1AC1SOFTWAREASN A:469 , LEU A:470 , SER A:471 , PHE A:639BINDING SITE FOR RESIDUE GOL A 801
2AC2SOFTWARESER B:17 , THR B:35 , GNP B:201 , HOH B:301 , HOH B:302BINDING 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 , 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:301 , HOH B:302 , HOH B:320BINDING SITE FOR RESIDUE GNP B 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:652 -His A:653

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HDQ)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.hhhhhhhhhhhhh...hhhhhh.eeeeee....eee.....hhhhhhhhhhhhhhhhh..hhhhh..eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee.........eeeeeeee...eeeeee.....eeeeee....eeee.....eeeeee....eeeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hdq A  419 YEKVRIYRMDGSYRSVELKHGNNTTVQQIMEGMRLSQETQQYFTIWICSENLSLQLKPYHKPLQHVRDWPEILAELTNLDPQRETPQLFLRRDVRLPLEVEKQIEDPLAILILFDEARYNLLKGFYTAPDAKLITLASLLLQIVYGNYESKKHKQGFLNEENLKSIVPVTKLKSKAPHWTNRILHEYKNLSTSEGVSKEMHHLQRMFLQNCWEIPTYGAAFFTGQIFTKASPSNHKVIPVYVGVNIKGLHLLNMETKALLISLKYGCFMWQLGDTDTCFQIHSMENKMSFIVHTKQAGLVVKLLMKLNGQL  729
                                   428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728 


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee.....hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hdq B    1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR  167
                                    10        20        30        40        50        60 ||     73        83        93       103       113       123       133       143       153       163    
                                                                                        62|                                                                                                     
                                                                                         66                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:5
                                      
               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
                4hdq C 1377 RRDYF 1381
   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 4HDQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (66, 79)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:652 - His A:653   [ RasMol ]  
 

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  4hdq
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  HEG1_HUMAN | Q9ULI3
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  KRIT1_HUMAN | O00522
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  RAP1B_HUMAN | P61224
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  KRIT1_HUMAN | O00522
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEG1_HUMAN | Q9ULI3: 3u7d
        KRIT1_HUMAN | O00522: 3u7d 4dx8 4dxa 4hdo 4jif 4tkn 5d68
        RAP1B_HUMAN | P61224: 3brw 3cf6 4dxa 4hdo 4m8n 4mgi 4mgk 4mgy 4mgz 4mh0 5kho

(-) Related Entries Specified in the PDB File

4hdo KRIT1 FERM DOMAIN + RAP1B