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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RABGAP DOMAIN OF THE RABGAP1L PROTEIN
 
Authors :  L. Nedyalkova, W. Tempel, Y. Tong, N. Zhong, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  23 Jun 09  (Deposition) - 14 Jul 09  (Release) - 14 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics Consortium, Gtpase Activating Protein, Sgc, Alternative Splicing, Gtpase Activation, Phosphoprotein, Polymorphism, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Nedyalkova, W. Tempel, Y. Tong, N. Zhong, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Rabgap Domain Of The Rabgap1L Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAB GTPASE-ACTIVATING PROTEIN 1-LIKE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid562
    GeneRABGAP1L, HHL, KIAA0471
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRABGAP1L

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 55)

Asymmetric Unit (2, 55)
No.NameCountTypeFull Name
1MSE23Mod. Amino AcidSELENOMETHIONINE
2UNX32Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2UNX14Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2UNX4Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 3 (2, 22)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2UNX14Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3HZJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HZJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HZJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HZJ)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBC_RABGAPPS50086 TBC/rab GAP domain profile.RBG1L_HUMAN538-724
 
 
  3A:538-724
B:538-724
C:538-724
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBC_RABGAPPS50086 TBC/rab GAP domain profile.RBG1L_HUMAN538-724
 
 
  1A:538-724
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBC_RABGAPPS50086 TBC/rab GAP domain profile.RBG1L_HUMAN538-724
 
 
  1-
B:538-724
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBC_RABGAPPS50086 TBC/rab GAP domain profile.RBG1L_HUMAN538-724
 
 
  1-
-
C:538-724

(-) Exons   (0, 0)

(no "Exon" information available for 3HZJ)

(-) 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:287
 aligned with RBG1L_HUMAN | Q5R372 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:287
                                   520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       
          RBG1L_HUMAN   511 YSWGELLGKWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGCHDNQAMLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHMPEEQAFCVLVKIMYDYGLRDLYRNNFEDLHCKFYQLERLMQEQLPDLHSHFSDLNLEAHMYASQWFLTLFTAKFPLCMVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLMEQACNIKVPTKKLKKYEKEYQTMR 797
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhh.............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------TBC_RABGAP  PDB: A:538-724 UniProt: 538-724                                                                                                                                                ------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hzj A 511 YSWGELLGKWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGCHDNQAmLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHmPEEQAFCVLVKImYDYGLRDLYRNNFEDLHCKFYQLERLmQEQLPDLHSHFSDLNLEAHmYASQWFLTLFTAKFPLCmVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLmEQACNIKVPTKKLKKYEKEYQTmR 797
                                   520       530       540       550       560       570       580       590       600       610       620       630   |   640      |650       660       670   |   680       690   |   700       710 |     720       730       740       750       760       770  |    780       790     | 
                                                                           560-MSE                                                                   634-MSE      647-MSE                    674-MSE             694-MSE           712-MSE                                                      773-MSE                796-MSE

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with RBG1L_HUMAN | Q5R372 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:267
                                   540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       
          RBG1L_HUMAN   531 LSTLVKSGVPEALRAEVWQLLAGCHDNQAMLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHMPEEQAFCVLVKIMYDYGLRDLYRNNFEDLHCKFYQLERLMQEQLPDLHSHFSDLNLEAHMYASQWFLTLFTAKFPLCMVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLMEQACNIKVPTKKLKKYEKEYQTMR 797
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhhh-----------hhhhhh.....hhhhhhhhhhh............hhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------TBC_RABGAP  PDB: B:538-724 UniProt: 538-724                                                                                                                                                ------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hzj B 531 LSTLVKSGVPEALRAEVWQLL-----------RYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHmPEEQAFCVLVKImYDYGLRDLYRNNFEDLHCKFYQLERLmQEQLPDLHSHFSDLNLEAHmYASQWFLTLFTAKFPLCmVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLmEQACNIKVPTKKLKKYEKEYQTmR 797
                                   540       550|        -  |    570       580       590       600       610       620       630   |   640      |650       660       670   |   680       690   |   700       710 |     720       730       740       750       760       770  |    780       790     | 
                                              551         563                                                                    634-MSE      647-MSE                    674-MSE             694-MSE           712-MSE                                                      773-MSE                796-MSE

Chain C from PDB  Type:PROTEIN  Length:288
 aligned with RBG1L_HUMAN | Q5R372 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:288
                                   519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789        
          RBG1L_HUMAN   510 LYSWGELLGKWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGCHDNQAMLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHMPEEQAFCVLVKIMYDYGLRDLYRNNFEDLHCKFYQLERLMQEQLPDLHSHFSDLNLEAHMYASQWFLTLFTAKFPLCMVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLMEQACNIKVPTKKLKKYEKEYQTMR 797
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh......hhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------TBC_RABGAP  PDB: C:538-724 UniProt: 538-724                                                                                                                                                ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hzj C 510 LYSWGELLGKWHSNLGARPKGLSTLVKSGVPEALRAEVWQLLAGCHDNQAmLDRYRILITKDSAQESVITRDIHRTFPAHDYFKDTGGDGQESLYKICKAYSVYDEDIGYCQGQSFLAAVLLLHmPEEQAFCVLVKImYDYGLRDLYRNNFEDLHCKFYQLERLmQEQLPDLHSHFSDLNLEAHmYASQWFLTLFTAKFPLCmVFHIIDLLLCEGLNIIFHVALALLKTSKEDLLQADFEGALKFFRVQLPKRYRAEENARRLmEQACNIKVPTKKLKKYEKEYQTmR 797
                                   519       529       539       549       559|      569       579       589       599       609       619       629    |  639       649       659       669    |  679       689    |  699       709  |    719       729       739       749       759       769   |   779       789      | 
                                                                            560-MSE                                                                   634-MSE      647-MSE                    674-MSE             694-MSE           712-MSE                                                      773-MSE                796-MSE

   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 3HZJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HZJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HZJ)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RBG1L_HUMAN | Q5R372)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0017137    Rab GTPase binding    Interacting selectively and non-covalently with Rab protein, any member of the Rab subfamily of the Ras superfamily of monomeric GTPases.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0090630    activation of GTPase activity    Any process that initiates the activity of an inactive GTPase through the replacement of GDP by GTP.
    GO:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0032880    regulation of protein localization    Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
    GO:0031338    regulation of vesicle fusion    Any process that modulates the frequency, rate or extent of vesicle fusion.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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