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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SMALL GTPASE GEM (GEMDNDCAM) IN COMPLEX TO MG.GDP
 
Authors :  A. Splingard, J. Menetrey, M. Perderiset, J. Cicolari, F. Hamoudi, L. Cabanie, A. El Marjou, A. Wells, A. Houdusse, J. De Gunzburg
Date :  09 Apr 06  (Deposition) - 09 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  G-Protein, Nucleotide-Binding, Gtp-Binding, Small Gtpase, Conformational Change, Cysteine-Modified, G-Protein Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Splingard, J. Menetrey, M. Perderiset, J. Cicolari, K. Regazzoni, F. Hamoudi, L. Cabanie, A. El Marjou, A. Wells, A. Houdusse, J. De Gunzburg
Biochemical And Structural Characterization Of The Gem Gtpase.
J. Biol. Chem. V. 282 1905 2007
PubMed-ID: 17107948  |  Reference-DOI: 10.1074/JBC.M604363200

(-) Compounds

Molecule 1 - GTP-BINDING PROTEIN GEM
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentG DOMAIN, RESIDUES 74-261
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGEM, GTP-BINDING MITOGEN-INDUCED T-CELL PROTEIN, RAS-LIKE PROTEIN KIR
 
Molecule 2 - GTP-BINDING PROTEIN GEM
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentG DOMAIN, RESIDUES 74-261
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGEM, GTP-BINDING MITOGEN-INDUCED T-CELL PROTEIN, RAS-LIKE PROTEIN KIR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CAS7Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:89 , GDP A:999 , HOH A:2008 , HOH A:2024 , HOH A:2028 , HOH A:2081BINDING SITE FOR RESIDUE MG A1000
2AC2SOFTWARESER B:89 , GDP B:999 , HOH B:2007 , HOH B:2024 , HOH B:2045 , HOH B:2046BINDING SITE FOR RESIDUE MG B1000
3AC3SOFTWAREGLN A:84 , GLY A:85 , VAL A:86 , GLY A:87 , LYS A:88 , SER A:89 , THR A:90 , ASN A:191 , LYS A:192 , ASP A:194 , LEU A:195 , PHE A:213 , SER A:221 , ALA A:222 , ALA A:223 , MG A:1000 , HOH A:2024 , HOH A:2028 , HOH A:2045 , HOH A:2076 , HOH A:2077 , HOH A:2079 , HOH A:2080 , HOH A:2081BINDING SITE FOR RESIDUE GDP A 999
4AC4SOFTWAREGLU B:83 , GLY B:85 , VAL B:86 , GLY B:87 , LYS B:88 , SER B:89 , THR B:90 , ASN B:191 , LYS B:192 , ASP B:194 , LEU B:195 , SER B:221 , ALA B:222 , ALA B:223 , MG B:1000 , HOH B:2024 , HOH B:2045 , HOH B:2046BINDING SITE FOR RESIDUE GDP B 999

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RASPS51421 small GTPase Ras family profile.GEM_HUMAN70-296  1B:70-261

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003961941aENSE00002127584chr8:95274578-95274433146GEM_HUMAN-00--
1.3bENST000003961943bENSE00001088912chr8:95272740-95272401340GEM_HUMAN1-1111112A:73-111 (gaps)
B:70-111 (gaps)
39
42
1.4ENST000003961944ENSE00001088910chr8:95265340-9526526477GEM_HUMAN111-136262A:111-135
B:111-135
25
25
1.5ENST000003961945ENSE00001088914chr8:95264451-95264247205GEM_HUMAN137-205692A:140-205
B:143-205
66
63
1.6bENST000003961946bENSE00002114213chr8:95262815-952614811335GEM_HUMAN205-296922A:205-258
B:205-261
54
57

(-) 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:178
 aligned with GEM_HUMAN | P55040 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:186
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
            GEM_HUMAN    73 NTYYRVVLIGEQGVGKSTLANIFAGVHDSMDSDCEVLGEDTYERTLMVDGESATIILLDMWENKGENEWLHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVSEGRACAVVFDCKFIETSAAVQHNVKELFEGIVRQVRLRRDSKEKNERRLAYQKR 258
               SCOP domains d2cjwa_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2cjwA00 A:73-258 P-loop conta    ining nucleotide triphosphate     hydrolases                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee.....hhhhhhhhhhhhh..----hhhhh..eeeeeeee..eeeeeeee.....----..hhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhh..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE RAS  PDB: - UniProt: 70-296                                                                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:73-111 (gaps)        -------------------------Exon 1.5  PDB: A:140-205 UniProt: 137-205 [INCOMPLETE]               ----------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.4  PDB: A:111-135  --------------------------------------------------------------------Exon 1.6b  PDB: A:205-258 UniProt: 205-296             Transcript 1 (2)
                 2cjw A  73 MTYYRVVLIGEQGVGKSTLANIFAGVHDS----cEVLGEDTYERTLMVDGESATIILLDMWEN----EWLHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRcREVSVSEGRAcAVVFDcKFIETSAAVQHNVKELFEGIVRQVRLRRDSKEKNERRLAYQKR 258
                                    82        92        |-   |   112       122       132  |    142       152       162       172       182       192     | 202      |212  |    222       232       242       252      
                                                      101    |                          135  140                                                       198-CAS    209-CAS |                                           
                                                           106-CAS                                                                                                      215-CAS                                       

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with GEM_HUMAN | P55040 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:192
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
            GEM_HUMAN    70 ESGNTYYRVVLIGEQGVGKSTLANIFAGVHDSMDSDCEVLGEDTYERTLMVDGESATIILLDMWENKGENEWLHDHCMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRCREVSVSEGRACAVVFDCKFIETSAAVQHNVKELFEGIVRQVRLRRDSKEKNERRLAYQKRKES 261
               SCOP domains d2cjwb_ B: automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2cjwB00 B:70-261 P-loop conta            ining nucleotide triphosp       hate hydrolases                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee....hhhhhhhhhhh.------------..eeeeeeee..eeeeeeee.....-------..hhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh......eeeeee...hhhhh..hhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE RAS  PDB: B:70-261 UniProt: 70-296                                                                                                                                                               PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:70-111 (gaps)           -------------------------Exon 1.5  PDB: B:143-205 UniProt: 137-205 [INCOMPLETE]               -------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.4  PDB: B:111-135  --------------------------------------------------------------------Exon 1.6b  PDB: B:205-261 UniProt: 205-296 [INCOMPLETE]   Transcript 1 (2)
                 2cjw B  70 EFGMTYYRVVLIGEQGVGKSTLANIFAGV------------EDTYERTLMVDGESATIILLDMWEN-------HDHcMQVGDAYLIVYSITDRASFEKASELRIQLRRARQTEDIPIILVGNKSDLVRcREVSVSEGRAcAVVFDCKFIETSAAVQHNVKELFEGIVRQVRLRRDSKEKNERRLAYQKRKES 261
                                    79        89        |-         - |     119       129     |   -   |  |149       159       169       179       189       199       209       219       229       239       249       259  
                                                       98          111                     135     143  |                                                 198-CAS    209-CAS                                                
                                                                                                      146-CAS                                                                                                               

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GEM_HUMAN | P55040)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0051276    chromosome organization    A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0051310    metaphase plate congression    The alignment of chromosomes at the metaphase plate (spindle equator), a plane halfway between the poles of the spindle.
    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:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    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.
    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.
    GO:0051233    spindle midzone    The area in the center of the spindle where the spindle microtubules from opposite poles overlap.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GEM_HUMAN | P550402g3y 2ht6

(-) Related Entries Specified in the PDB File

2ht6 CRYSTAL STRUCTURE OF HUMAN GEM G-DOMAIN BOUND TO GDP