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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF NUP133 REVEALS A BETA-PROPELLER FOLD COMMON TO SEVERAL NUCLEOPORINS
 
Authors :  I. C. Berke, T. Boehmer, G. Blobel, T. U. Schwartz
Date :  29 Sep 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Propeller, Helical Insertions, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. C. Berke, T. Boehmer, G. Blobel, T. U. Schwartz
Structural And Functional Analysis Of Nup133 Domains Reveal Modular Building Blocks Of The Nuclear Pore Complex.
J. Cell Biol. V. 167 591 2004
PubMed-ID: 15557116  |  Reference-DOI: 10.1083/JCB.200408109

(-) Compounds

Molecule 1 - NUCLEAR PORE COMPLEX PROTEIN NUP133
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21 CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNUP133
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEOPORIN NUP133, 133 KDA NUCLEOPORIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1XKS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:364 -Pro A:365

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric/Biological Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030829T106PNU133_HUMANPolymorphism428231AT106P
2UniProtVAR_030830I294VNU133_HUMANPolymorphism11805194AI294V
3UniProtVAR_035854G326VNU133_HUMANUnclassified  ---AG326V
4CancerSNPVAR_NU133_HUMAN_CCDS1579_1_01 *G326VNU133_HUMANDisease (Breast cancer)  ---AG326V
5UniProtVAR_030831Q406RNU133_HUMANPolymorphism1065674AQ406R
6UniProtVAR_035855G448RNU133_HUMANUnclassified  ---AG448R
7CancerSNPVAR_NU133_HUMAN_CCDS1579_1_02 *G448RNU133_HUMANDisease (Breast cancer)  ---AG448R
   * ID not provided by source

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002613961aENSE00001263815chr1:229644088-229643815274NU133_HUMAN1-61610--
1.2ENST000002613962ENSE00001069992chr1:229641905-229641787119NU133_HUMAN61-101411A:75-10127
1.3ENST000002613963ENSE00001069983chr1:229637849-229637746104NU133_HUMAN101-135351A:101-13535
1.4ENST000002613964ENSE00001069988chr1:229636610-229636503108NU133_HUMAN136-171361A:136-171 (gaps)36
1.5ENST000002613965ENSE00001069985chr1:229635565-229635431135NU133_HUMAN172-216451A:172-216 (gaps)45
1.7ENST000002613967ENSE00001069978chr1:229634053-229633883171NU133_HUMAN217-273571A:217-273 (gaps)57
1.8ENST000002613968ENSE00001069994chr1:229631794-229631639156NU133_HUMAN274-325521A:274-32552
1.9ENST000002613969ENSE00001069984chr1:229631312-22963124271NU133_HUMAN326-349241A:326-34924
1.10ENST0000026139610ENSE00001069987chr1:229625849-229625702148NU133_HUMAN349-398501A:349-39850
1.11ENST0000026139611ENSE00001015850chr1:229623360-229623213148NU133_HUMAN399-448501A:399-44850
1.12ENST0000026139612ENSE00001015859chr1:229622275-229622118158NU133_HUMAN448-500531A:448-47730
1.13ENST0000026139613ENSE00000961359chr1:229619892-22961980192NU133_HUMAN501-531310--
1.14ENST0000026139614ENSE00000594035chr1:229613507-229613344164NU133_HUMAN531-586560--
1.15ENST0000026139615ENSE00000793031chr1:229611479-22961138595NU133_HUMAN586-617320--
1.16ENST0000026139616ENSE00000793030chr1:229606551-229606327225NU133_HUMAN618-692750--
1.17ENST0000026139617ENSE00000961360chr1:229602503-229602381123NU133_HUMAN693-733410--
1.18ENST0000026139618ENSE00000594038chr1:229601266-229601167100NU133_HUMAN734-767340--
1.19cENST0000026139619cENSE00001015853chr1:229600622-229600371252NU133_HUMAN767-851850--
1.20ENST0000026139620ENSE00000961361chr1:229599423-229599290134NU133_HUMAN851-895450--
1.21aENST0000026139621aENSE00000961362chr1:229596516-229596358159NU133_HUMAN896-948530--
1.22ENST0000026139622ENSE00000961363chr1:229594043-229593908136NU133_HUMAN949-994460--
1.23ENST0000026139623ENSE00000961364chr1:229588390-229588272119NU133_HUMAN994-1033400--
1.24cENST0000026139624cENSE00000961365chr1:229586352-22958627281NU133_HUMAN1034-1060270--
1.25aENST0000026139625aENSE00000961366chr1:229584937-22958487365NU133_HUMAN1061-1082220--
1.26ENST0000026139626ENSE00000961367chr1:229580749-22958066189NU133_HUMAN1082-1112310--
1.27cENST0000026139627cENSE00001879885chr1:229577787-229577045743NU133_HUMAN1112-1156450--

(-) Sequences/Alignments

Asymmetric/Biological 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:374
 aligned with NU133_HUMAN | Q8WUM0 from UniProtKB/Swiss-Prot  Length:1156

    Alignment length:403
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474   
          NU133_HUMAN    75 ESVNYDVKTFGSSLPVKVMEALTLAEVDDQLTINIDEGGWACLVCKEKLIIWKIALSPITKLSVCKELQLPPSDFHWSADLVALSYSSPSGEAHSTQAVAVMVATREGSIRYWPSLAGEDTYTEAFVDSGGDKTYSFLTAVQGGSFILSSSGSQLIRLIPESSGKIHQHILPQGQGMLSGIGRKVSSLFGILSPSSDLTLSSVLWDRERSSFYSLTSSNISKWELDDSSEKHAYSWDINRALKENITDAIWGSESNYEAIKEGVNIRYLDLKQNCDGLVILAAAWHSADNPCLIYYSLITIEDNGCQMSDAVTVEVTQYNPPFQSEDLILCQLTVPNFSNQTAYLYNESAVYVCSTGTGKFSLPQEKIVFNAQGDSVLGAGACGGVPIIFSRNSGLVSITSRE 477
               SCOP domains d1xksa_ A: Nuclear pore complex protein Nup133                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1xksA00 A:75-477 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains Nucleoporin_N-1xksA01 A:75-472                                                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh.....eeeee....eeeeee..eeeeee.....hhhhh.eeeee........hhh.eeeee..-------...eeeeee....eeeee.........eeee.----...eeeeeee...eeeeee....eeeeee.....eeeee.......------------------....eeeeeee....eeeeee..eeeeeee....eeeeeeeehhhhhhhhhhhhhhh...hhhhhhh..eeeeeeeeee..eeeeeeeee........eeeeeeee..........eeeee........hhhhh..eee.......eeeee...eeeeee..........eeee.hhhhh.eeeeeee..eeeeee...eeeeeee.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------V-------------------------------------------------------------------------------R-----------------------------------------R----------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-------------------------------------------------------------------------------------------------------------------------R----------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:75-101    ----------------------------------Exon 1.4  PDB: A:136-171 (gaps)     Exon 1.5  PDB: A:172-216 (gaps)              Exon 1.7  PDB: A:217-273 (gaps) UniProt: 217-273         Exon 1.8  PDB: A:274-325 UniProt: 274-325           -----------------------Exon 1.10  PDB: A:349-398 UniProt: 349-398        Exon 1.11  PDB: A:399-448 UniProt: 399-448        ----------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.3  PDB: A:101-135           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:326-349--------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:448-477      Transcript 1 (2)
                 1xks A  75 ESVNYDVKTFGSSLPVKVMEALTLAEVDDQLTINIDEGGWACLVCKEKLIIWKIALSPITKLSVCKELQLPPSDFHWSADLVALSYSS-------TQAVAVMVATREGSIRYWPSLAGEDTYTEAFV----DKTYSFLTAVQGGSFILSSSGSQLIRLIPESSGKIHQHILPQGQGM------------------SDLTLSSVLWDRERSSFYSLTSSNISKWELDDSSEKHAYSWDINRALKENITDAIWGSESNYEAIKEGVNIRYLDLKQNCDGLVILAAAWHSADNPCLIYYSLITIEDNGCQMSDAVTVEVTQYNPPFQSEDLILCQLTVPNFSNQTAYLYNESAVYVCSTGTGKFSLPQEKIVFNAQGDSVLGAGACGGVPIIFSRNSGLVSITSRE 477
                                    84        94       104       114       124       134       144       154       | -     | 174       184       194      |  - |     214       224       234       244      |  -         -     | 274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474   
                                                                                                                 162     170                            201  206                                          251                270                                                                                                                                                                                                               

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NU133_HUMAN | Q8WUM0)
molecular function
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    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.
biological process
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    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:0021915    neural tube development    The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium.
    GO:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0031081    nuclear pore distribution    Any process that establishes the spatial arrangement of nuclear pores within the nuclear envelope.
    GO:0006999    nuclear pore organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.
    GO:0048339    paraxial mesoderm development    The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0061053    somite development    The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    GO:0000972    transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery    The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript.
    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:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0000940    condensed chromosome outer kinetochore    The region of a condensed chromosome kinetochore most external to centromeric DNA; this outer region mediates kinetochore-microtubule interactions.
    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:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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:0031080    nuclear pore outer ring    A subcomplex of the nuclear pore complex (NPC) that forms the outer rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two outer rings each contain multiple copies of the following proteins: Nup133p, Nup120p, Nup145Cp, Nup85p, Nup84p, Seh1p, and Sec13p. In vertebrates, the two outer rings each contain multiple copies of the following proteins: Nup133, Nup160, Nup96, Nup75, Nup107, Seh1, Sec13, Nup43, Nup37, and ALADIN. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup84 complex (S. cerevisiae) or the Nup107-160 complex (vertebrates).
    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
        NU133_HUMAN | Q8WUM03cqc 3cqg 3i4r 5a9q

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