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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND RAN-BINDING DOMAIN FROM HUMAN RANBP2
 
Authors :  J. P. Geyer, R. Doeker, W. Kremer, X. Zhao, J. Kuhlmann, H. R. Kalbitzer
Date :  28 Sep 04  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta Barrel, Pleckstrin-Homology (Ph) Domain, Phosphotyrosine-Binding (Ptb) Domain, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. P. Geyer, R. Doker, W. Kremer, X. Zhao, J. Kuhlmann, H. R. Kalbitzer
Solution Structure Of The Ran-Binding Domain 2 Of Ranbp2 And Its Interaction With The C Terminus Of Ran.
J. Mol. Biol. V. 348 711 2005
PubMed-ID: 15826666  |  Reference-DOI: 10.1016/J.JMB.2005.02.033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAN-BINDING PROTEIN 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRAN-BINDING DOMAIN 2 (RANBD2)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRANBP2, NUCLEAR PORE COMPLEX PROTEIN NUP358, NUCLEOPORIN NUP358, 358 KDA NUCLEOPORIN, P270

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XKE)

(-) Sites  (0, 0)

(no "Site" information available for 1XKE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XKE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XKE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XKE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XKE)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002831951bENSE00001427934chr2:109335937-109336134198RBP2_HUMAN1-24240--
1.3aENST000002831953aENSE00001628671chr2:109345588-10934565568RBP2_HUMAN25-47230--
1.5bENST000002831955bENSE00001658463chr2:109347230-109347341112RBP2_HUMAN47-84380--
1.6aENST000002831956aENSE00001642732chr2:109347778-109347930153RBP2_HUMAN85-135510--
1.7bENST000002831957bENSE00001779112chr2:109351988-109352218231RBP2_HUMAN136-212770--
1.8ENST000002831958ENSE00001730926chr2:109352560-109352705146RBP2_HUMAN213-261490--
1.9ENST000002831959ENSE00001785652chr2:109356945-109357137193RBP2_HUMAN261-325650--
1.10ENST0000028319510ENSE00001713500chr2:109363167-10936325488RBP2_HUMAN326-355300--
1.11aENST0000028319511aENSE00001718980chr2:109365376-109365585210RBP2_HUMAN355-425710--
1.12ENST0000028319512ENSE00001776974chr2:109367720-109367901182RBP2_HUMAN425-485610--
1.13aENST0000028319513aENSE00001779700chr2:109367984-109368159176RBP2_HUMAN486-544590--
1.13eENST0000028319513eENSE00001761857chr2:109368327-109368450124RBP2_HUMAN544-585420--
1.14bENST0000028319514bENSE00001718984chr2:109369454-109369615162RBP2_HUMAN586-639540--
1.15ENST0000028319515ENSE00001757154chr2:109369882-109370019138RBP2_HUMAN640-685460--
1.16ENST0000028319516ENSE00001624597chr2:109370281-109370427147RBP2_HUMAN686-734490--
1.17ENST0000028319517ENSE00001686256chr2:109371361-109371540180RBP2_HUMAN735-794600--
1.18ENST0000028319518ENSE00001591933chr2:109371632-10937171584RBP2_HUMAN795-822280--
1.19ENST0000028319519ENSE00001791450chr2:109374869-109375004136RBP2_HUMAN823-868460--
1.20ENST0000028319520ENSE00001684879chr2:109378557-10937865195RBP2_HUMAN868-899320--
1.21aENST0000028319521aENSE00001147357chr2:109379693-1093848445152RBP2_HUMAN900-261717181A:1-130130
1.22ENST0000028319522ENSE00001009418chr2:109388157-109388327171RBP2_HUMAN2617-2674580--
1.23ENST0000028319523ENSE00001009429chr2:109388945-10938903793RBP2_HUMAN2674-2705320--
1.24ENST0000028319524ENSE00001291545chr2:109389324-109389502179RBP2_HUMAN2705-2764600--
1.25ENST0000028319525ENSE00001009419chr2:109392188-109392392205RBP2_HUMAN2765-2833690--
1.26ENST0000028319526ENSE00001009428chr2:109393586-109393687102RBP2_HUMAN2833-2867350--
1.27ENST0000028319527ENSE00001377207chr2:109397725-109397885161RBP2_HUMAN2867-2920540--
1.28ENST0000028319528ENSE00001383394chr2:109398584-109398857274RBP2_HUMAN2921-3012920--
1.29ENST0000028319529ENSE00001147257chr2:109398984-109399318335RBP2_HUMAN3012-31231120--
1.30bENST0000028319530bENSE00001316371chr2:109400052-1094022672216RBP2_HUMAN3124-32241010--

(-) Sequences/Alignments

NMR Structure
   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:130
 aligned with RBP2_HUMAN | P49792 from UniProtKB/Swiss-Prot  Length:3224

    Alignment length:130
                                  2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145      2155
          RBP2_HUMAN   2026 VTGEEDEKVLYSQRVKLFRFDAEVSQWKERGLGNLKILKNEVNGKLRMLMRREQVLKVCANHWITTTMNLKPLSGSDRAWMWLASDFSDGDAKLEQLAAKFKTPELAEEFKQKFEECQRLLLDIPLQTPH 2155
               SCOP domains ------d1xkea1 A:7-124 Ran-binding protein 2                                                                                 ------ SCOP domains
               CATH domains 1xkeA00 A:1-130 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                                        CATH domains
               Pfam domains --Ran_BP1-1xkeA01 A:3-120                                                                                               ---------- Pfam domains
         Sec.struct. author ......eee...eeeeeeeee....eeeeeeeeeeeeeee.....eeeeeee....eeeeeee......eee.......eeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.21a  PDB: A:1-130 UniProt: 900-2617 [INCOMPLETE]                                                                            Transcript 1
                1xke A    1 GSGEEDEKVLYSQRVKLFRFDAEVSQWKERGLGNLKILKNEVNGKLRMLMRREQVLKVCANHWITTTMNLKPLSGSDRAWMWLASDFSDGDAKLEQLAAKFKTPELAEEFKQKFEECQRLLLDIPLQTPK  130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PH (111)

(-) Gene Ontology  (39, 39)

NMR Structure(hide GO term definitions)
Chain A   (RBP2_HUMAN | P49792)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008536    Ran GTPase binding    Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
    GO:0019789    SUMO transferase activity    Catalysis of the transfer of SUMO from one protein to another via the reaction X-SUMO + Y --> Y-SUMO + X, where both X-SUMO and Y-SUMO are covalent linkages.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0033132    negative regulation of glucokinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of glucokinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a glucose molecule.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0090526    regulation of gluconeogenesis involved in cellular glucose homeostasis    Any process that modulates the frequency, rate or extent of gluconeogenesis as an integral part of cellular glucose homeostasis.
    GO:0010827    regulation of glucose transport    Any process that modulates the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    GO:0044615    nuclear pore nuclear basket    A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RBP2_HUMAN | P497921rrp 1z5s 2las 3uin 3uio 3uip 4ga0 4i9y 4l6e 4lqw 5cll 5clq

(-) Related Entries Specified in the PDB File

5159 CHEMICAL SHIFT ASSIGNMENT