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(-) Description

Title :  RASIP1 RA DOMAIN IN COMPLEX WITH RAP1B
 
Authors :  A. R. Gingras
Date :  15 Jun 16  (Deposition) - 19 Oct 16  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rasip1, Ras-Association Domain, Rap1B, Complex, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Gingras, W. Puzon-Mclaughlin, A. A. Bobkov, M. H. Ginsberg
Structural Basis Of Dimeric Rasip1 Ra Domain Recognition Of The Ras Subfamily Of Gtp-Binding Proteins.
Structure V. 24 2152 2016
PubMed-ID: 27839947  |  Reference-DOI: 10.1016/J.STR.2016.10.001

(-) Compounds

Molecule 1 - RAS-INTERACTING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: RASIP1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAIN
 
Molecule 2 - RAS-RELATED PROTEIN RAP-1B
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: RAP1B, OK/SW-CL.11
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GTP-BINDING PROTEIN SMG P21B

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:206 , ARG A:227 , VAL A:238 , TRP A:242 , ARG A:250 , ASP B:206 , ARG B:227 , TRP B:242binding site for residue GOL A 301
2AC2SOFTWARESER C:17 , THR C:35 , GNP C:201 , HOH C:302 , HOH C:303binding site for residue MG C 200
3AC3SOFTWAREGLU B:258 , GLY 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:200 , HOH C:302 , HOH C:303binding site for residue GNP C 201
4AC4SOFTWARESER D:17 , THR D:35 , GNP D:201 , HOH D:301 , HOH D:302binding site for residue MG D 200
5AC5SOFTWAREGLY D:13 , VAL D:14 , GLY D:15 , LYS D:16 , SER D:17 , ALA D:18 , PHE D:28 , VAL D:29 , GLU D:30 , TYR D:32 , THR D:35 , GLY D:60 , ASN D:116 , LYS D:117 , ASP D:119 , LEU D:120 , SER D:147 , ALA D:148 , MG D:200 , HOH D:301 , HOH D:302binding site for residue GNP D 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KHO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KHO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KHO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KHO)

(-) Exons   (0, 0)

(no "Exon" information available for 5KHO)

(-) 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:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......eeeeeeee....hhhhhhhhhhh.....hhh.eeeeeeee......eeee.....hhhhhhhheee....eeeeeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5kho A 143 APPGVLKIFGAGLASGANYKSVLATARSTARELVAEALERYGLSCVDAFALCDALGRPWRAEHLRVLGDSERPLLVQELWRARPGWARRFELRGREEARRLEQ 265
                                   152       162       172       182  ||   203       222       232       242       252       262   
                                                                    185|           211|                                            
                                                                     197            221                                            


Chain B from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......eeeeeee.....hhhhhhhhhhhhhh..hhhh.eeeeeeee......eeee.....hhhhhhhheee....eeeeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5kho B 143 APPGVLKIFGAGLASGANYKSVLATARSTARELVAEALERYGLSSCVDAFALCDALGRPWRAEHLRVLGDSERPLLVQELWRARPGWARRFELRGREEARRLEQEA 267
                                   152       162       172       182  ||   202       221       231       241       251       261      
                                                                    185|            211|                                              
                                                                     196             221                                              


Chain C from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhh............eeeeeeee....eeeeeeee.....hhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhh..hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kho C   1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162     
                                                                                       61|                                                                                                       
                                                                                        64                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhh...........eeeeeeee....eeeeeeee.........hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhh..hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kho D   1 MREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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 5KHO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KHO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KHO)

(-) Gene Ontology  (32, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5kho
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  RAIN_HUMAN | Q5U651
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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
        RAIN_HUMAN | Q5U651: 5khq
        RAP1B_HUMAN | P61224: 3brw 3cf6 4dxa 4hdo 4hdq 4m8n 4mgi 4mgk 4mgy 4mgz 4mh0

(-) Related Entries Specified in the PDB File

5khq