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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RAD GTPASE
 
Authors :  A. Yanuar, S. Sakurai, K. Kitano, T. Hakoshima
Date :  18 May 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rad, Gtpase, Small-G, Rgk, Signal Transduction, Diabetes, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Yanuar, S. Sakurai, K. Kitano, T. Hakoshima
Crystal Structure Of Human Rad Gtpase Of The Rgk-Family
Genes Cells V. 11 961 2006
PubMed-ID: 16866878  |  Reference-DOI: 10.1111/J.1365-2443.2006.00994.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN RAD
    ChainsA, B
    EC Number3.6.5.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPROEX-HT
    Expression System StrainBL21 STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentGTPASE DOMAIN
    GeneRRAD, RAD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAS ASSOCIATED WITH DIABETES, RAD1, RAD GTPASE

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:51 , HOH A:52 , HOH A:53 , HOH A:54 , SER A:105 , GDP A:500BINDING SITE FOR RESIDUE MG A 400
2AC2SOFTWAREHOH B:56 , HOH B:57 , HOH B:58 , HOH B:59 , SER B:105 , GDP B:500BINDING SITE FOR RESIDUE MG B 400
3AC3SOFTWAREHOH A:16 , HOH A:25 , HOH A:42 , HOH A:51 , HOH A:52 , HOH A:53 , HOH A:72 , GLY A:101 , VAL A:102 , GLY A:103 , LYS A:104 , SER A:105 , ALA A:106 , ASN A:203 , LYS A:204 , ASP A:206 , LEU A:207 , SER A:233 , ALA A:234 , ALA A:235 , MG A:400 , ASP B:206 , LEU B:207 , GDP B:500BINDING SITE FOR RESIDUE GDP A 500
4AC4SOFTWAREGDP A:500 , HOH B:57 , HOH B:58 , HOH B:59 , HOH B:66 , HOH B:70 , HOH B:71 , GLY B:101 , VAL B:102 , GLY B:103 , LYS B:104 , SER B:105 , ALA B:106 , ASN B:203 , LYS B:204 , ASP B:206 , LEU B:207 , SER B:233 , ALA B:234 , ALA B:235 , MG B:400BINDING SITE FOR RESIDUE GDP B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DPX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DPX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DPX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DPX)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002997591aENSE00001943321chr16:66959547-66959312236RAD_HUMAN-00--
1.2bENST000002997592bENSE00001104552chr16:66959097-66958713385RAD_HUMAN1-1241242A:90-115
B:92-115
26
24
1.3ENST000002997593ENSE00001104559chr16:66957822-6695774974RAD_HUMAN124-148252A:125-146
B:125-146
22
22
1.4ENST000002997594ENSE00001104564chr16:66957623-66957419205RAD_HUMAN149-217692A:154-217 (gaps)
B:161-217 (gaps)
64
57
1.5aENST000002997595aENSE00001931509chr16:66956256-66955588669RAD_HUMAN217-308922A:217-254
B:217-254
38
38

(-) 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:146
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:165
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     
            RAD_HUMAN    90 SVYKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLR 254
               SCOP domains d2dpxa_ A: automated match         es                                                                                                                                 SCOP domains
               CATH domains 2dpxA00 A:90-254 P-loop co         ntaining nucleotide tr       iphosphate hydrolases                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh..---------.eeeeeeee..eeeeeeee...-------hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh---...eeeeee..........hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:90-115           ------------------------Exon 1.4  PDB: A:154-217 (gaps) UniProt: 149-217 [INCOMPLETE]        ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:125-146 --------------------------------------------------------------------Exon 1.5a  PDB: A:217-254 [INCOMPLETE] Transcript 1 (2)
                 2dpx A  90 SVYKVLLLGAPGVGKSALARIFGGVE---------HTYDRSIVVDGEEASLMVYDIW-------LPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRAR---DVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLR 254
                                    99       109     |   -     | 129       139      |  -    |  159       169       179       189 |   | 199       209       219       229       239       249     
                                                   115       125                  146     154                                  191 195                                                           

Chain B from PDB  Type:PROTEIN  Length:135
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:163
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
            RAD_HUMAN    92 YKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLR 254
               SCOP domains d2dpxb_ B: automated mat         ches                                                                                                                               SCOP domains
               CATH domains 2dpxB00 B:92-254 P-loop          containing nucleotide               triphosphate hydrolases                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhh..---------.eeeeeeee..eeeeeeee...--------------...eeeeeee..hhhhhhhhhhhhhhhhhh-----..eeeeee...hhhhh..hhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:92-115         ------------------------Exon 1.4  PDB: B:161-217 (gaps) UniProt: 149-217 [INCOMPLETE]        ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.3  PDB: B:125-146 --------------------------------------------------------------------Exon 1.5a  PDB: B:217-254 [INCOMPLETE] Transcript 1 (2)
                 2dpx B  92 YKVLLLGAPGVGKSALARIFGGVE---------HTYDRSIVVDGEEASLMVYDIW--------------MGDAYVIVYSVTDKGSFEKASELRVQLRRA-----VPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLR 254
                                   101       111   |     -   |   131       141    |    -       161       171       181        |-    |  201       211       221       231       241       251   
                                                 115       125                  146            161                          190   196                                                          

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DPX)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RAD_HUMAN | P55042)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        RAD_HUMAN | P550422gjs 3q72 3q7p 3q7q

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