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(-) Description

Title :  CRYSTAL STRUCTURE OF RAB GTPASE SEC4P MUTANT - S29V
 
Authors :  F. C. Rinadi, R. N. Collins
Date :  09 Apr 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Gtpase, Gdp Bound, Rab, 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, B
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3ZN3Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:29 , GLY A:30 , VAL A:31 , GLY A:32 , LYS A:33 , SER A:34 , CYS A:35 , PHE A:45 , PRO A:47 , ASN A:133 , LYS A:134 , ASP A:136 , MET A:137 , SER A:162 , ALA A:163 , LYS A:164 , MG A:202 , HOH A:314 , HOH A:318 , HOH A:360 , HOH A:374 , HOH A:380 , HOH A:401binding site for residue GDP A 201
2AC2SOFTWARESER A:34 , GDP A:201 , HOH A:314 , HOH A:318 , HOH A:380 , HOH A:422binding site for residue MG A 202
3AC3SOFTWAREASP A:43 , ASP A:166 , HOH A:404 , ILE B:85 , HIS B:121binding site for residue ZN A 203
4AC4SOFTWAREVAL B:29 , GLY B:30 , VAL B:31 , GLY B:32 , LYS B:33 , SER B:34 , CYS B:35 , PRO B:47 , ASN B:133 , LYS B:134 , ASP B:136 , MET B:137 , SER B:162 , ALA B:163 , LYS B:164 , MG B:202 , HOH B:310 , HOH B:318 , HOH B:323 , HOH B:356 , HOH B:382 , HOH B:397binding site for residue GDP B 201
5AC5SOFTWARESER B:34 , GDP B:201 , HOH B:323 , HOH B:356 , HOH B:382 , HOH B:391binding site for residue MG B 202
6AC6SOFTWAREILE A:85 , HIS A:121 , HOH A:302 , ASP B:43 , ASP B:166 , HOH B:366binding site for residue ZN B 203
7AC7SOFTWAREASP B:56 , GLU B:182 , HOH B:344 , HOH B:444binding site for residue ZN B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z8Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z8Y)

(-) 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:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhh.......eeeeeeee..eeeeeeee.......hhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z8y A  19 SIMKILLIGDVGVGKSCLLVRFVEDKFNPGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKI 184
                                    28        38        54        64        74        84        94       104       114       124       134       144       154       164       174       184
                                                       47|                                                                                                                                  
                                                        54                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhh....hhhhhh...eeeeeeee..eeeeeeeee..........hhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z8y B  19 SIMKILLIGDVGVGKSCLLVRFVEDKFNPSFITTIGIDFKIKTVDINGKKVKLQLWDTAGQERFRTITTAYYRGAMGIILVYDVTDERTFTNIKQWFKTVNEHANDEAQLLLVGNKSDMETRVVTADQGEALAKELGIPFIESSAKNDDNVNEIFFTLAKLIQEKID 185
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178
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  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 4Z8Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z8Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z8Y)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)

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  4z8y
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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
        SEC4_YEAST | P07560: 1g16 1g17 2eqb 2ocy 3cph 4zdw

(-) Related Entries Specified in the PDB File

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