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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RAB GTPASE SEC4P MUTANT - S29V IN COMPLEX WITH SEC2P AND GDP
 
Authors :  F. C. Rinadi, R. N. Collins
Date :  20 Apr 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gtpase, Gdp Bound, Rab Sec4P, Sec2P, Gtp Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. C. Rinaldi, M. Packer, R. Collins
New Insights Into The Molecular Mechanism Of The Rab Gtpase Sec4P Activation.
Bmc Struct. Biol. V. 15 14 2015
PubMed-ID: 26263895  |  Reference-DOI: 10.1186/S12900-015-0041-5

(-) Compounds

Molecule 1 - RAS-RELATED PROTEIN SEC4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPSUMO
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SEC4, SRO6, YFL005W
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: SUPPRESSOR OF RHO3 PROTEIN 6
 
Molecule 2 - RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR SEC2
    Chains: B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: SEC2, YNL272C, N0641
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GDP-GTP EXCHANGE FACTOR SEC2

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:28 , VAL A:29 , GLY A:30 , GLY A:32 , LYS A:33 , SER A:34 , CYS A:35 , ASN A:133 , LYS A:134 , ASP A:136 , MET A:137 , SER A:162 , ALA A:163 , LYS A:164 , HOH A:303 , HOH A:306binding site for residue GDP A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:50 -Asn B:51

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDW)

(-) 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:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhh.............eeee...........eeee.....hhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh....ee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdw A  19 SIMKILLIGDVGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKIDSN 187
                                    28        38        48        58      ||71        81        91       101       111       121       131       141       151       161       171       181      
                                                                         65|                                                                                                                      
                                                                          69                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4zdw B  50 SNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREK 140
                                    59        69        79        89        99       109       119       129       139 


Chain C from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 4zdw C  50 SNYNQLKEDYNTLKRELSDRDDEVKRLREDIAKENELRTKAEEEADKLNKEVEDLTASLFDEANNMVADARKEKYAIEILNKRLTEQLREK 140
                                    59        69        79        89        99       109       119       129       139
   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 4ZDW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ser B:50 - Asn B:51   [ RasMol ]  
 

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  4zdw
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  SEC2_YEAST | P17065
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  SEC4_YEAST | P07560
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 Related Entries

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

UniProtKB/Swiss-Prot
        SEC2_YEAST | P17065: 2e7s 2eqb 2ocy
        SEC4_YEAST | P07560: 1g16 1g17 2eqb 2ocy 3cph 4z8y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4ZDW)