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(-) Description

Title :  MOLECULAR CHARACTERIZATION OF THE RAN BINDING ZINC FINGER DOMAIN
 
Authors :  M. M. Higa, S. L. Alam, W. I. Sundquist, K. S. Ullman
Date :  20 Apr 06  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc Finger, Ran, Nuclear Pore, Zinc Knuckle, Nucleoporin, Pore, Transport, Nup153, Nup358, Ranbp2, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. M. Higa, S. L. Alam, W. I. Sundquist, K. S. Ullman
Molecular Characterization Of The Ran-Binding Zinc Finger Domain Of Nup153.
J. Biol. Chem. V. 282 17090 2007
PubMed-ID: 17426026  |  Reference-DOI: 10.1074/JBC.M702715200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR PORE COMPLEX PROTEIN NUP153
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T VARIANT WITH TEV CLEAVAGE SITE
    Expression System StrainBL21(DE3) CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSECOND ZINC FINGER, RESIDUES 722-750
    GeneNUP153
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEOPORIN NUP153, 153 KDA NUCLEOPORIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:9 , CYS A:12 , CYS A:23 , CYS A:26BINDING SITE FOR RESIDUE ZN A 32

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RANBP2_2PS50199 Zinc finger RanBP2 type profile.NU153_HUMAN657-687
722-751
793-822
851-880
  1-
A:3-31
-
-
2ZF_RANBP2_1PS01358 Zinc finger RanBP2-type signature.NU153_HUMAN662-681
726-745
797-816
855-874
  1-
A:7-26
-
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002620771bENSE00001927997chr6:17706618-17706508111NU153_HUMAN1-37370--
1.2ENST000002620772ENSE00000848155chr6:17688849-17688627223NU153_HUMAN38-112750--
1.3ENST000002620773ENSE00000848154chr6:17676001-17675753249NU153_HUMAN112-195840--
1.4ENST000002620774ENSE00000848153chr6:17675599-17675460140NU153_HUMAN195-241470--
1.5ENST000002620775ENSE00000848152chr6:17675264-17675136129NU153_HUMAN242-284430--
1.6ENST000002620776ENSE00000848151chr6:17669777-17669661117NU153_HUMAN285-323390--
1.7ENST000002620777ENSE00000848150chr6:17669568-1766952445NU153_HUMAN324-338150--
1.8ENST000002620778ENSE00000848149chr6:17669259-1766920654NU153_HUMAN339-356180--
1.9ENST000002620779ENSE00000848148chr6:17665616-17665470147NU153_HUMAN357-405490--
1.10ENST0000026207710ENSE00000848147chr6:17662301-1766224953NU153_HUMAN406-423180--
1.11ENST0000026207711ENSE00000848146chr6:17662010-17661884127NU153_HUMAN423-465430--
1.13ENST0000026207713ENSE00000848145chr6:17649531-17649394138NU153_HUMAN466-511460--
1.14ENST0000026207714ENSE00000848144chr6:17648136-1764803899NU153_HUMAN512-544330--
1.15ENST0000026207715ENSE00000848143chr6:17646385-1764629888NU153_HUMAN545-574300--
1.16ENST0000026207716ENSE00000848142chr6:17640295-17640170126NU153_HUMAN574-616430--
1.17ENST0000026207717ENSE00000848141chr6:17638001-17637384618NU153_HUMAN616-8222071A:0-31 (gaps)35
1.18ENST0000026207718ENSE00000848140chr6:17633075-17632881195NU153_HUMAN822-887660--
1.19ENST0000026207719ENSE00000848139chr6:17629770-17628886885NU153_HUMAN887-11822960--
1.20ENST0000026207720ENSE00000848138chr6:17626395-17626039357NU153_HUMAN1182-13011200--
1.21ENST0000026207721ENSE00000848137chr6:17625064-17624792273NU153_HUMAN1301-1392920--
1.22ENST0000026207722ENSE00000848136chr6:17616926-17616758169NU153_HUMAN1392-1448570--
1.23ENST0000026207723ENSE00000848135chr6:17616412-176152691144NU153_HUMAN1448-1475280--

(-) 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:32
 aligned with NU153_HUMAN | P49790 from UniProtKB/Swiss-Prot  Length:1475

    Alignment length:35
                                   725       735       745     
          NU153_HUMAN   716 GDKFKPVIGTWDCDTCLVQNKPEAIKCVACETPKP 750
               SCOP domains ------d2gqea1 A:3-31                SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .---......ee......ee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                PROSITE (1) ------ZF_RANBP2_2  PDB: A:3-31      PROSITE (1)
                PROSITE (2) ----------ZF_RANBP2_1         ----- PROSITE (2)
               Transcript 1 Exon 1.17  PDB: A:0-31 (gaps)       Transcript 1
                 2gqe A   0 G---HMVIGTWDCDTCLVQNKPEAIKCVACETPKP  31
                            |   |    6        16        26     
                            |   1                              
                            0                                  

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

NMR Structure(hide GO term definitions)
Chain A   (NU153_HUMAN | P49790)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008139    nuclear localization sequence binding    Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    GO:0043495    protein anchor    Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific membrane location.
    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:0017056    structural constituent of nuclear pore    The action of a molecule that contributes to the structural integrity of the nuclear pore complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    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:0046832    negative regulation of RNA export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of RNA from the nucleus into the cytoplasm.
    GO:0051292    nuclear pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.
    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: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: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:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0075732    viral penetration into host nucleus    The crossing by the virus of the host nuclear membrane, either as naked viral genome or for small viruses as an intact capsid.
    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:0005642    annulate lamellae    Stacks of endoplasmic reticulum (ER) membranes containing a high density of nuclear pores, thought to form from excess nuclear membrane components, that have been described in a number of different cells. Annulate lamellar membranes are continuous with and embedded within the ER.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0034399    nuclear periphery    The portion of the nuclear lumen proximal to the inner nuclear membrane.
    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: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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NU153_HUMAN | P497902ebq 2ebr 2ebv 4u0c 4u0d

(-) Related Entries Specified in the PDB File

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7158
1nj3 STRUCTURE AND UBIQUITIN INTERACTIONS OF THE CONSERVED NZF DOMAIN OF NPL4
1q5w UBIQUITIN RECOGNITION BY NPL4 ZINC-FINGERS