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(-) Description

Title :  CRYSTAL STRUCTURE OF GDP-BOUND HUMAN GIMAP2, AMINO ACID RESIDUES 21-260
 
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 :  2.80
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 21-260
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIMMUNITY-ASSOCIATED PROTEIN 2, HIMAP2, GIMAP2

 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
1AC1SOFTWARETHR B:31 , GLY B:32 , THR B:33 , GLY B:34 , LYS B:35 , SER B:36 , ALA B:37 , SER B:50 , LYS B:51 , LEU B:52 , HIS B:147 , GLU B:149 , PHE B:182 , ASN B:184 , ARG B:185 , MG B:1255BINDING SITE FOR RESIDUE GDP B1254
2AC2SOFTWARESER B:36 , GLU B:49 , GDP B:1254BINDING SITE FOR RESIDUE MG B1255
3AC3SOFTWAREGLY 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 , PHE A:182 , ASN A:183 , ASN A:184 , ARG A:185 , MG A:1257BINDING SITE FOR RESIDUE GDP A1256
4AC4SOFTWARESER A:36 , GDP A:1256BINDING SITE FOR RESIDUE MG A1257

(-) SS Bonds  (0, 0)

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

(-) 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 2XTO)

(-) Exons   (0, 0)

(no "Exon" information available for 2XTO)

(-) 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:224
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:235
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKCGPVGSDERVKEFKQSLIKYMETQRSYTA 255
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh.................eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.hhhh.eeeeeehhhhhh..hhhhhhhh..hhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh.-----------hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xto A  21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQ-----------RVKEFKQSLIKYMETQRSYTA 255
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      -    |  240       250     
                                                                                                                                                                                                                                    223         235                    

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with GIMA2_HUMAN | Q9UG22 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          GIMA2_HUMAN    21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQRSKCGPVGSDERVKEFKQSLIKYMETQRSY 253
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --AIG1-2xtoB01 B:23-223                                                                                                                                                                                    ------------------------------ Pfam domains (1)
           Pfam domains (2) --AIG1-2xtoB02 B:23-223                                                                                                                                                                                    ------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhh.................eeeeeee..eeeeeee.hhhhhh.....hhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhh.eeeeeehhhhhh..hhhhhhhh..hhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh-----------hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------F-----------------------------------------------------------------------------S--------R-------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xto B  21 SELRIILVGKTGTGKSAAGNSILRKQAFESKLGSQTLTKTCSKSQGSWGNREIVIIDTPDMFSWKDHCEALYKEVQRCYLLSAPGPHVLLLVTQLGRYTSQDQQAAQRVKEIFGEDAMGHTIVLFTHKEDLNGGSLMDYMHDSDNKALSKLVAACGGRICAFNNRAEGSNQDDQVKELMDCIEDLLMEKNGDHYTNGLYSLIQ-----------RVKEFKQSLIKYMETQRSY 253
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      -    |  240       250   
                                                                                                                                                                                                                                    223         235                  

   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 2XTO)

(-) CATH Domains  (0, 0)

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

(-) 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 | Q9UG222xtm 2xtn 2xtp 3p1j

(-) Related Entries Specified in the PDB File

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