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(-) Description

Title :  CRYSTAL STRUCTURE OF GDP-BOUND HUMAN GIMAP2, AMINO ACID RESIDUES 1-234
 
Authors :  D. Schwefel, C. Froehlich, O. Daumke
Date :  11 Oct 10  (Deposition) - 20 Oct 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immune System, G Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Schwefel, C. Froehlich, J. Eichhorst, B. Wiesner, J. Behlke, L. Aravind, O. Daumke
Structural Basis Of Oligomerization In Septin-Like Gtpase Of Immunity-Associated Protein 2 (Gimap2)
Proc. Natl. Acad. Sci. Usa V. 107 20299 2010
PubMed-ID: 21059949  |  Reference-DOI: 10.1073/PNAS.1010322107
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTPASE IMAP FAMILY MEMBER 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P1
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-234
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGIMAP2, IMMUNITY-ASSOCIATED PROTEIN 2, HIMAP2

 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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL3Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL3Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , THR A:33 , GLY A:34 , LYS A:35 , SER A:36 , ALA A:37 , SER A:50 , LYS A:51 , LEU A:52 , HIS A:147 , GLU A:149 , ASN A:184 , ARG A:185 , MG A:1229 , HOH A:2114 , HOH A:2188 , HOH A:2189 , HOH A:2191 , HOH A:2193 , HOH A:2194BINDING SITE FOR RESIDUE GDP A1228
2AC2SOFTWARESER A:36 , GDP A:1228 , HOH A:2011 , HOH A:2059 , HOH A:2189 , HOH A:2191BINDING SITE FOR RESIDUE MG A1229
3AC3SOFTWAREGLU A:131 , ILE A:132 , GLY A:134 , ASN A:216 , GLY A:217 , LEU A:218 , GOL A:1231 , HOH A:2195 , HOH A:2196BINDING SITE FOR RESIDUE GOL A1230
4AC4SOFTWAREGLY A:217 , GOL A:1230 , HOH A:2197 , HOH A:2198 , GLU B:131 , ILE B:132 , GLY B:134 , ASN B:216 , GLY B:217 , LEU B:218BINDING SITE FOR RESIDUE GOL A1231
5AC5SOFTWARESER A:62 , LYS A:63 , ARG A:97 , LEU A:101 , HOH A:2199 , HOH A:2200 , GLU B:208 , LYS B:209 , HOH B:2079BINDING SITE FOR RESIDUE GOL A1232
6AC6SOFTWAREGLY B:32 , THR B:33 , GLY B:34 , LYS B:35 , SER B:36 , ALA B:37 , SER B:50 , HIS B:147 , GLU B:149 , ASN B:183 , ASN B:184 , MG B:1228 , HOH B:2019BINDING SITE FOR RESIDUE GDP B1227
7AC7SOFTWARESER B:36 , THR B:58 , GDP B:1227 , HOH B:2015 , HOH B:2019BINDING SITE FOR RESIDUE MG B1228

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:103 -Pro A:104
2Ala B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049531V74FGIMA2_HUMANPolymorphism11558054A/BV74F
2UniProtVAR_049532N152SGIMA2_HUMANPolymorphism17173567A/BN152S
3UniProtVAR_017305H161RGIMA2_HUMANPolymorphism2075078A/BH161R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049531V74FGIMA2_HUMANPolymorphism11558054AV74F
2UniProtVAR_049532N152SGIMA2_HUMANPolymorphism17173567AN152S
3UniProtVAR_017305H161RGIMA2_HUMANPolymorphism2075078AH161R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049531V74FGIMA2_HUMANPolymorphism11558054BV74F
2UniProtVAR_049532N152SGIMA2_HUMANPolymorphism17173567BN152S
3UniProtVAR_017305H161RGIMA2_HUMANPolymorphism2075078BH161R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XTM)

(-) 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:207
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:207
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKC 227
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh.................eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhh.eeeeeehhhhhh..hhhhhhhhh.hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xtm A  21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKC 227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:206
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSK 226
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --AIG1-2xtmB01 B:23-226                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) --AIG1-2xtmB02 B:23-226                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh......-------....eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhh.eeeeeehhhhhh..hhhhhhhhh.hhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xtm B  21 SELRIILVGKTGTGKSAAGNSILRKQAFES-------TKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSK 226
                                    30        40        50       |60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                        50      58                                                                                                                                                                        

   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 2XTM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XTM)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GIMA2_HUMAN | Q9UG22)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GIMA2_HUMAN | Q9UG222xtn 2xto 2xtp 3p1j

(-) Related Entries Specified in the PDB File

2xtn CRYSTAL STRUCTURE OF GTP-BOUND HUMAN GIMAP2 , AMINO ACID RESIDUES 1-234
2xto CRYSTAL STRUCTURE OF GDP-BOUND HUMAN GIMAP2 , AMINO ACID RESIDUES 21-260
2xtp CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE HUMAN GIMAP2, AMINO ACID RESIDUES 1-260