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(-) Description

Title :  ARA7-GDP-CA2+/VPS9A
 
Authors :  K. Ihara
Date :  09 Jul 12  (Deposition) - 27 Feb 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gtpase-Gdp-Metal-Gef Complex, Vps9 Domain, Ras Super Family, Guanine Nucleotide Exchange Factor, Small Gtpase, Gdp/Gtp Binding, Divalent Metal Binding, Geranylgeranylation, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Uejima, K. Ihara, M. Sunada, M. Kawasaki, T. Ueda, R. Kato, A. Nakano S. Wakatsuki
Direct Metal Recognition By Guanine Nucleotide-Exchange Factor In The Initial Step Of The Exchange Reaction
Acta Crystallogr. , Sect. D V. 69 345 2013
PubMed-ID: 23519409  |  Reference-DOI: 10.1107/S0907444912047294

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 9A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VPS9 DOMAIN, UNP RESIDUES 1-265
    Gene: VPS9A
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: VPS9A, ATVSP9A
 
Molecule 2 - RAS-RELATED PROTEIN RABF2B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SMALL GTPASE, UNP RESIDUES 1-179
    Gene: ARA-7
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ARA7, ATRABF2B, RAS-RELATED PROTEIN ARA-7, RAS-RELATED PROTEIN RAB5B, ATRAB5B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:182 , ASP A:185 , HOH A:404 , HOH A:410 , HOH A:485 , SER B:24 , GDP B:200BINDING SITE FOR RESIDUE CA A 300
2AC2SOFTWAREASN A:180 , CA A:300 , HOH A:404 , HOH A:485 , GLY B:20 , ALA B:21 , GLY B:22 , LYS B:23 , SER B:24 , SER B:25 , ASN B:123 , LYS B:124 , ASP B:126 , LEU B:127 , SER B:153 , ALA B:154 , LYS B:155 , HOH B:322 , HOH B:375BINDING SITE FOR RESIDUE GDP B 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G01)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn B:55 -Asp B:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G01)

(-) Exons   (0, 0)

(no "Exon" information available for 4G01)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g01 A  26 VKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPLWSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQQFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVINNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRESKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR 262
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains d4g01b_ B: automated matches                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhh..eee...eeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g01 B   8 SINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLP 172
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G01)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G01)

(-) Gene Ontology  (24, 28)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAF2B_ARATH | Q9SN68: 2efc 2efd 2efe 2efh
        VPS9A_ARATH | Q9LT31: 2efc 2efd 2efe 2efh

(-) Related Entries Specified in the PDB File

2efc ARA7-GDP/VPS9A
2efd ARA7/VPS9A
2efe ARA7-GDPNH2/VPS9A
2efh ARA7-GDP/VPS9A(D185N)