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(-) Description

Title :  CRYSTAL STRUCTURE OF RIAM RA-PH DOMAINS IN COMPLEX WITH GTP BOUND RAP1
 
Authors :  H. Zhang, Y. E. Chang, M. L. Brennan, J. Wu
Date :  22 May 13  (Deposition) - 05 Mar 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ras-Related Protein, Ubiquitin Fold, Gtpase, Actin Polymerization, Integrin Activation, Cell Adhesion, Riam, Rapl, Mst1, Pdk, Rap1, Ena/Vasp, Profilin, Membrane, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhang, Y. C. Chang, M. L. Brennan, J. Wu
The Structure Of Rap1 In Complex With Riam Reveals Specificity Determinants And Recruitment Mechanism.
J Mol Cell Biol V. 6 128 2014
PubMed-ID: 24287201  |  Reference-DOI: 10.1093/JMCB/MJT044

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN RAP-1A
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET281
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-167
    GeneKREV1, RAP1A
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC21KG, G-22K, GTP-BINDING PROTEIN SMG P21A, RAS-RELATED PROTEIN KREV-1
 
Molecule 2 - AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET281
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRA-PH DOMAINS (UNP RESIDUES 179-437)
    GeneAPBB1IP, PREL1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymAPBB1-INTERACTING PROTEIN 1, PROLINE-RICH EVH1 LIGAND 1, PREL-1, PROLINE-RICH PROTEIN 48

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:12 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , ALA A:18 , PHE A:28 , VAL A:29 , GLU A:30 , 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:147 , ALA A:148 , LYS A:149 , MG A:202 , HOH A:305 , HOH A:308 , HOH A:358 , HOH A:387 , HOH A:412 , HOH A:413BINDING SITE FOR RESIDUE GTP A 201
2AC2SOFTWARESER A:17 , THR A:35 , GTP A:201 , HOH A:412 , HOH A:413BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREPHE B:306 , CYS B:307 , TYR B:427 , ASP B:428 , HOH B:718 , HOH B:802 , LYS D:374BINDING SITE FOR RESIDUE EDO B 501
4AC4SOFTWAREGLY C:13 , VAL C:14 , GLY C:15 , LYS C:16 , SER C:17 , ALA C:18 , PHE C:28 , VAL C:29 , GLU C:30 , TYR C:32 , PRO C:34 , THR C:35 , GLY C:60 , ASN C:116 , LYS C:117 , ASP C:119 , LEU C:120 , SER C:147 , ALA C:148 , LYS C:149 , MG C:202 , HOH C:306 , HOH C:332 , HOH C:333BINDING SITE FOR RESIDUE GTP C 201
5AC5SOFTWARESER C:17 , THR C:35 , GTP C:201 , HOH C:332 , HOH C:333BINDING SITE FOR RESIDUE MG C 202
6AC6SOFTWAREHOH A:317 , LYS B:374 , PHE D:306 , CYS D:307 , LYS D:424 , TYR D:427 , ASP D:428 , HOH D:723 , HOH D:733BINDING SITE FOR RESIDUE EDO D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr B:352 -Ser B:353

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KVG)

(-) Sequences/Alignments

Asymmetric 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:165
                                                                                                                                                                                                     
               SCOP domains d4kvga_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee....hhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvg A   0 HMREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                     9        19        29        39        49        59 ||     72        82        92       102       112       122       132       142       152       162     
                                                                                        61|                                                                                                      
                                                                                         65                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeee...hhhhhhhhhhhhhh......eeeeeee....eeee.....hhhhhhh........eeeeee....hhhhhhhhhh...hhhhhhhhhhhhhh.........eeeeeee......eeeeeeee...eeee............eeeee.hhheeeee.hhhhhhh.....eeeee...........eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kvg B 178 MKKLVVKVHMDDSSTKSLMVDERQLARDVLDNLFEKTHCDCNVDWCLYEIYPELQIERVFEDHENVVEVLSDWTRDTENKVLFLEKEERYAVFKNPQNFYLMNAKNKEYLLEESFCGTSIIVPELEGALYLKEDGKKSWKRRYFLLRASGIYYVPKGKTKTSRDLACFIQFENVNIYYGIQCKMKYKAPTDHCFVLKHPQIQKESQYIKYLCCDDARTLSQWVMGIRIAKYGKTLYDNYQRAVARA 437
                                   187       197       207       217       227       237       247       257       267       277||     301       311       321       331       341       351       361       371       381       391       401       411       421       431      
                                                                                                                              278|                                                                                                                                                
                                                                                                                               293                                                                                                                                                

Chain C from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4kvgc_ C: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....hhhhhhhhhhhh..........eeeeeeeeee..eeeeeeeeee....hhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvg C   1 MREYKLVVLGSVGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQIN 166
                                    10        20        30        40        50        60||      76        86        96       106       116       126       136       146       156       166
                                                                                       61|                                                                                                  
                                                                                        68                                                                                                  

Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeeeeee...hhhhhhhhhhhhhh......eeeeeee....eeee.....hhhhhhh........eeeeee....hhhhhhhhhh....hhhhhhhhhhhhhh.........eeeeeee......eeeeeeee...eeeee............eeee.hhheeeee.hhhhhhh.....eeeee...........eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvg D 178 MKKLVVKVHMDDSSTKSLMVDERQLARDVLDNLFEKTHCDCNVDWCLYEIYPELQIERVFEDHENVVEVLSDWTRDTENKVLFLEKEERYAVFKNPQNFYLDMNAKNKEYLLEESFCGTSIIVPELEGALYLKEDGKKSWKRRYFLLRASGIYYVPKGKTKTSRDLACFIQFENVNIYYGIQCKMKYKAPTDHCFVLKHPQIQKESQYIKYLCCDDARTLSQWVMGIRIAKYGKTLYDNYQRAVARA 437
                                   187       197       207       217       227       237       247       257       267       277 ||    300       310       320       330       340       350       360       370       380       390       400       410       420       430       
                                                                                                                               279|                                                                                                                                                
                                                                                                                                293                                                                                                                                                

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 63)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AB1IP_MOUSE | Q8R5A33tca 4w8p
        RAP1A_HUMAN | P628341c1y 1gua 3kuc

(-) Related Entries Specified in the PDB File

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