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(-) Description

Title :  CRYSTAL STRUCTURE OF RAD G-DOMAIN-GTP ANALOG COMPLEX
 
Authors :  Y. Sasson, L. Navon-Perry, J. A. Hirsch
Date :  05 Jan 11  (Deposition) - 21 Sep 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  G-Domain, G-Protein, Cav2 Beta, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sasson, L. Navon-Perry, D. Huppert, J. A. Hirsch
Rgk Family G-Domain:Gtp Analog Complex Structures And Nucleotide-Binding Properties.
J. Mol. Biol. V. 413 372 2011
PubMed-ID: 21903096  |  Reference-DOI: 10.1016/J.JMB.2011.08.017

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN RAD
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21D
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentG-DOMAIN, RESIDUES 90-255
    GeneRRAD, RAD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAD1, RAS ASSOCIATED WITH DIABETES

 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
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:8 , HOH B:20 , HOH B:30 , HOH B:31 , PRO B:100 , 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:257BINDING SITE FOR RESIDUE GNP B 256
2AC2SOFTWAREHOH B:30 , HOH B:31 , SER B:105 , GLU B:147 , GNP B:256BINDING SITE FOR RESIDUE MG B 257
3AC3SOFTWAREHOH A:28 , HOH A:29 , GLY A:101 , VAL A:102 , GLY A:103 , LYS A:104 , SER A:105 , ALA A:106 , GLU A:147 , ASN A:203 , LYS A:204 , ASP A:206 , LEU A:207 , SER A:233 , ALA A:234 , ALA A:235 , MG A:257BINDING SITE FOR RESIDUE GNP A 256
4AC4SOFTWAREHOH A:28 , HOH A:29 , SER A:105 , GLU A:147 , GNP A:256BINDING SITE FOR RESIDUE MG A 257

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q7P)

(-) 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:90-113
B:90-115
24
26
1.3ENST000002997593ENSE00001104559chr16:66957822-6695774974RAD_HUMAN124-148252A:125-147
B:125-147
23
23
1.4ENST000002997594ENSE00001104564chr16:66957623-66957419205RAD_HUMAN149-217692A:158-217 (gaps)
B:160-217 (gaps)
60
58
1.5aENST000002997595aENSE00001931509chr16:66956256-66955588669RAD_HUMAN217-308922A:217-255
B:217-255
39
39

(-) 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:142
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:166
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            RAD_HUMAN    90 SVYKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
               SCOP domains d3q7pa_ A: automated mat           ches                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhh.-----------.eeeee........eeeee....----------......eeeeeee..hhhhhhhhhhhhhhhhhhh---...eeeeee..........hhhhhhhhhh....eeee.hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:90-113           ------------------------Exon 1.4  PDB: A:158-217 (gaps) UniProt: 149-217 [INCOMPLETE]        -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:125-147 --------------------------------------------------------------------Exon 1.5a  PDB: A:217-255 [INCOMPLETE]  Transcript 1 (2)
                 3q7p A  90 SVYKVLLLGAPGVGKSALARIFGG-----------HTYDRSIVVDGEEASLMVYDIWE----------CMAMGDAYVIVYSVTDKGSFEKASELRVQLRRAR---DVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
                                    99       109   |     -     | 129       139       | -       159       169       179       189 |   | 199       209       219       229       239       249      
                                                 113         125                   147        158                              191 195                                                            

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with RAD_HUMAN | P55042 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:166
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249      
            RAD_HUMAN    90 SVYKVLLLGAPGVGKSALARIFGGVEDGPEAEAAGHTYDRSIVVDGEEASLMVYDIWEQDGGRWLPGHCMAMGDAYVIVYSVTDKGSFEKASELRVQLRRARQTDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
               SCOP domains d3q7pb_ B: automated match         es                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhh...---------.eeeeeeee..eeeeeeeee...------------....eeeeeee..hhhhhhhhhhhhhhhhhhh-.....eeeeee..........hhhhhhhhhh....eeee.hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:90-115           ------------------------Exon 1.4  PDB: B:160-217 (gaps) UniProt: 149-217 [INCOMPLETE]        -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: B:125-147 --------------------------------------------------------------------Exon 1.5a  PDB: B:217-255 [INCOMPLETE]  Transcript 1 (2)
                 3q7p B  90 SVYKVLLLGAPGVGKSALARIFGGVE---------HTYDRSIVVDGEEASLMVYDIWE------------AMGDAYVIVYSVTDKGSFEKASELRVQLRRAR-TDDVPIILVGNKSDLVRSREVSVDEGRACAVVFDCKFIETSAALHHNVQALFEGVVRQIRLRR 255
                                    99       109     |   -     | 129       139       | -         -|      169       179       189 | |   199       209       219       229       239       249      
                                                   115       125                   147          160                            191 |                                                              
                                                                                                                                 193                                                              

   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  (0, 0)

(no "CATH Domain" information available for 3Q7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q7P)

(-) 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

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

UniProtKB/Swiss-Prot
        RAD_HUMAN | P550422dpx 2gjs 3q72 3q7q

(-) Related Entries Specified in the PDB File

2dpx 3q72 3q7q