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(-) Description

Title :  CRYSTAL STRUCTURE OF LEPB GAP DOMAIN FROM LEGIONELLA DRANCOURTII IN COMPLEX WITH RAB1-GDP AND ALF3
 
Authors :  Q. Yu, Q. Yao, D. -C. Wang, F. Shao
Date :  26 Mar 13  (Deposition) - 08 May 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  New Gap Fold, Bind And Hydrolyze Guanosine Triphosphate, Rab1 Binding, Hydrolase Activator-Protein Transport Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Yu, L. Hu, Q. Yao, Y. Zhu, N. Dong, D. -C. Wang, F. Shao
Structural Analyses Of Legionella Lepb Reveal A New Gap Fol That Catalytically Mimics Eukaryotic Rasgap
Cell Res. V. 23 775 2013
PubMed-ID: 23588383  |  Reference-DOI: 10.1038/CR.2013.54

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: GAP DOMAIN, UNP RESIDUES 316-620
    Gene: LDG_7216
    Organism Scientific: LEGIONELLA DRANCOURTII
    Organism Taxid: 658187
    Strain: LLAP12
    Synonym: GTPASE ACTIVATING PROTEIN
 
Molecule 2 - RAS-RELATED PROTEIN RAB-1A
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-177
    Gene: RAB1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAS SUPERFAMILY OF MONOMERIC G PROTEIN, YPT1-RELATED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2AF31Ligand/IonALUMINUM FLUORIDE
3GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:540 , SER A:541 , ASP A:546 , ILE A:547 , ARG A:579BINDING SITE FOR RESIDUE ACY A 701
2AC2SOFTWAREARG A:447 , GLY B:21 , VAL B:22 , GLY B:23 , LYS B:24 , SER B:25 , CYS B:26 , TYR B:36 , GLU B:38 , TYR B:40 , THR B:43 , ASN B:124 , LYS B:125 , ASP B:127 , LEU B:128 , SER B:154 , ALA B:155 , LYS B:156 , AF3 B:401 , MG B:402BINDING SITE FOR RESIDUE GDP B 400
3AC3SOFTWAREARG A:447 , SER B:20 , GLY B:21 , LYS B:24 , SER B:42 , THR B:43 , GLY B:69 , GLN B:70 , GDP B:400 , MG B:402 , HOH B:502BINDING SITE FOR RESIDUE AF3 B 401
4AC4SOFTWARESER B:25 , THR B:43 , THR B:67 , GDP B:400 , AF3 B:401BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:410 -Asp A:411
2Glu A:494 -Asp A:495
3Asp A:495 -Asp A:496

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JVS)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.............hhhhh......ee..ee.....hhhhhhhhh.........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh..hhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvs A 331 ATPPLLQMEQEQPFPELIRTWAGLLGQIGVESVRTEEVNFGQLAKCFNDYLNTVAEHCEQQNIWQHKREENHNFFTAFKPDASKAALHGHAYIAHYKESVILRHLSIVDPKTLGMLRFAPYEAPSTDYCRHFPDSPWAKMQRLATAGQNIILQLRLIQNGQMLEDDLPVLQKALDDFMQYKTEVDALLAHDTPVSTHDSSFFYDIDEQTLNAMSGDQLATICFEELNAPHPSRLIMRILKSDSLWQEVDDSLNGDAFMGRQDDICEKRNKICQWRQLVQ 621
                                   340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490     ||505       515       525||     542       552       562       572       582       592       602       612         
                                                                                                                                                                                               496|                     526|                                                                                       
                                                                                                                                                                                                502                      534                                                                                       


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains d4jvsb_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhhhh......ee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeeee..........hhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvs B   7 EYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM 176
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176
   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 4JVS)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp A:495 - Asp A:496   [ RasMol ]  
    Glu A:494 - Asp A:495   [ RasMol ]  
    Pro A:410 - Asp A:411   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAB1A_HUMAN | P62820: 2fol 2wwx 3l0i 3sfv 3tkl 4fmb 4fmc 4fmd 4fme 4iru

(-) Related Entries Specified in the PDB File

4jw1