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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GTPASE IMAP FAMILY MEMBER 4
 
Authors :  Y. Shen, L. Nedyalkova, Y. Tong, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, D. W. Andrews, H. Park, Structural Genomics Consortium (Sgc)
Date :  25 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics Consortium, Sgc, Coiled Coil, Gtp- Binding, Nucleotide-Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shen, L. Nedyalkova, Y. Tong, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, A. Bochkarev, D. W. Andrews, H. Park
Crystal Structure Of Human Gtpase Imap Family Member 4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GTPASE IMAP FAMILY MEMBER 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 562
    Gene: GIMAP4, IAN1, IMAP4, MSTP062
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IMMUNITY-ASSOCIATED PROTEIN 4, IMMUNITY-ASSOCIATED NUCLEOTIDE 1 PROTEIN, IAN-1, HIAN1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE
4UNX2Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE
4UNX4Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:39 , GLY A:40 , ALA A:41 , GLY A:42 , LYS A:43 , SER A:44 , ALA A:45 , SER A:58 , ARG A:155 , ASP A:157 , LEU A:189 , ASN A:190 , ASN A:191 , LYS A:192 , HOH A:243 , HOH A:244 , HOH A:245 , MG A:402BINDING SITE FOR RESIDUE GDP A 401
2AC2SOFTWARESER A:44 , THR A:66 , HOH A:243 , HOH A:244 , HOH A:245 , GDP A:401BINDING SITE FOR RESIDUE MG A 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:69 -A:106

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:111 -Pro A:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017306E128DGIMA4_HUMANPolymorphism2293172AE128D
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017306E128DGIMA4_HUMANPolymorphism2293172AE128D
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LXX)

(-) 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:169
 aligned with GIMA4_HUMAN | Q9NUV9 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:193
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
          GIMA4_HUMAN    29 SQLRIVLVGKTGAGKSATGNSILGRKVFHSGTAAKSITKKCEKRSSSWKETELVVVDTPGIFDTEVPNAETSKEIIRCILLTSPGPHALLLVVPLGRYTEEEHKATEKILKMFGERARSFMILIFTRKDDLGDTNLHDYLREAPEDIQDLMDIFGDRYCALNNKATGAEQEAQRAQLLGLIQRVVRENKEGCY 221
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --AIG1-3lxxA01 A:31-221                                                                                                                                                                           Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhh......-------....eeeeeee..eeeeeee.....-----hhhhhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeehhhhh------------hhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lxx A  29 SQLRIVLVGKTGAGKSATGNSILGRKVFHS-------TKKCEKRSSSWKETELVVVDTPGIF-----NAETSKEIIRCILLTSPGPHALLLVVPLGRYTEEEHKATEKILKmFGERARSFmILIFTRKDDL------------PEDIQDLmDIFGDRYCALNNKATGAEQEAQRAQLLGLIQRVVRENKEGCY 221
                                    38        48        58       |68        78        88 |     |98       108       118       128       138 |     148|      158|        -   |   178|      188       198       208       218   
                                                        58      66                      90    96                                         140-MSE  149-MSE   159          172      |                                          
                                                                                                                                                                                179-MSE
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  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 3LXX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (GIMA4_HUMAN | Q9NUV9)
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  3lxx
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 Related Entries

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(-) Related Entries Specified in the PDB File

3lxw CRYSTAL STRUCTURE OF HUMAN GTPASE IMAP FAMILY MEMBER 1