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(-) Description

Title :  NUCLEOPORIN NUP120 FROM S.CEREVISIAE (AA 1-757)
 
Authors :  N. C. Leksa, S. G. Brohawn, T. U. Schwartz
Date :  21 Jun 09  (Deposition) - 28 Jul 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Protein, Coiled Coil, Membrane, Mrna Transport, Nuclear Pore Complex, Nucleus, Phosphoprotein, Protein Transport, Translocation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. C. Leksa, S. G. Brohawn, T. U. Schwartz
The Structure Of The Scaffold Nucleoporin Nup120 Reveals A New And Unexpected Domain Architecture.
Structure V. 17 1082 2009
PubMed-ID: 19576787  |  Reference-DOI: 10.1016/J.STR.2009.06.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOPORIN NUP120
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePET-DUET
    FragmentUNP RESIDUES 1-757
    GeneNUP120, RAT2, YKL057C, YKL314, YKL313
    Organism CommonBREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymNUCLEAR PORE PROTEIN NUP120

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3HXR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HXR)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Pro A:18 -Glu A:19
2Ser A:74 -Arg A:75
3Asn A:240 -Cys A:241
4Leu A:248 -Thr A:249
5Mse A:259 -Val A:260
6Leu A:293 -Glu A:294
7Gly A:467 -Asp A:468
8Ile A:602 -Ser A:603
9Ser A:603 -Ala A:604
10Asp A:608 -Gly A:609

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HXR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HXR)

(-) 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:660
 aligned with NU120_YEAST | P35729 from UniProtKB/Swiss-Prot  Length:1037

    Alignment length:731
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729 
          NU120_YEAST     - -MACLSRIDANLLQYYEKPEPNNTVDLYVSNNSNNNGLKEGDKSISTPVPQPYGSEYSNCLLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASMNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLEDGGLLGLKKVDGVHYEPLLFNDNSYLKSLTRFFSRSSKSDYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQDYDMVSQSDSDPSHFRKVEAVGEYLSLYNNTLVTLLPLENGLFQMGTLLVDSSGILTYTFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTKTGDVERGFCNLKSRYGTQIFERAQQILSENKIIMAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYNHSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSMTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQMKPGIFWKKDFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFFMTFFRSYIIE 730
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee............eeee...-----------------------...eeeeee.....eeeeee.....eeeeee........eeeee...........eeeee...eeeeeee.....eeeeeeehhhhhh........................eeeee...eeeee.....eeee..---------------.............--....eeeeeee...eeeeee....ee.......................--------....eeee..eeeeee.....eeeee.-----------................eeeeeeee...........eeeeeeeee..eeeeeeeeehhhhhh.eeee.....hhhhhhhhh.......--hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.eeeeeee...eeeeee....eeeeeee.hhhhhhhhh....----hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhh....------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hxr A   0 SmACLSRIDANLLQYYEKPEPNNTVDLYVS-----------------------GSEYSNCLLLSNSEYICYHFSSRSTLLTFYPLSDAYHGKTINIHLPNASmNQRYTLTIQEVEQQLLVNVILKDGSFLTLQLPLSFLFSSANTLNGEWFHLQNPYDFTVRVPHFLFYVSPQFSVVFLEDGGLLGLKK---------------YLKSLTRFFSRSS--DYDSVISCKLFHERYLIVLTQNCHLKIWDLTSFTLIQDYDmVSQSDSDP--------VGEYLSLYNNTLVTLLPLENGLFQmGT-----------TFQNNIPTNLSASAIWSIVDLVLTRPLELNVEASYLNLIVLWKSGTASKLQILNVNDESFKNYEWIESVNKSLVDLQSEHDLDIVTK--DVERGFCNLKSRYGTQIFERAQQILSENKIImAHNEDEEYLANLETILRDVKTAFNEASSITLYGDEIILVNCFQPYNHSLYKLNTTVENWFYNmHSE----ELFKYLRTLNGFASTLSNDVLRSISKKFLDIITGELPDSmTTVEKFTDIFKNCLENQFEITNLKILFDELNSFDIPVVLNDLINNQmKP------DFISAIKFDGFTSIISLESLHQLLSIHYRITLQVLLTFVLFDLDTEIFGQHISTLLDLHYKQFLLLNLYRQDKCLLAEVLLKDSSEFSFGVKFFNYGQLIAYIDSLNSNVYNASITENSFFmTFFRSYIIE 730
                             |       9        19        29         -         -   |    59        69        79        89        99  |    109       119       129       139       149       159       169       179        |-         -    |  209      |219       229       239       249       259       | -      |279       289       299| |      -    |  319       329       339       349       359       369       379       389       399|  |   409       419       429    |  439       449       459       469       479       489       499|    | 509       519       529       539    |  549       559       569       579       589 | |     -|      609       619       629       639       649       659       669       679       689       699       709       719 |     729 
                             |                          29                      53                                              102-MSE                                                                               188             204         216  |                                     259-MSE 267      276                     300-MSE       314                                                                                   400  |                            434-MSE                                                        497-MSE 505                                    544-MSE                                        591-MSE  600                                                                                                                      721-MSE     
                             1-MSE                                                                                                                                                                                                                   219                                                                                302                                                                                                  403                                                                                              500                                                                                          593                                                                                                                                         

   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 3HXR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HXR)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NU120_YEAST | P35729)
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:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0031990    mRNA export from nucleus in response to heat stress    The directed movement of mRNA from the nucleus to the cytoplasm during a heat stimulus, a temperature stimulus above the optimal temperature for the organism; in particular, a process that enables an organism withstand exposure to temperatures that would otherwise lethally impair poly(A)+ mRNA-nucleus export.
    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:0035392    maintenance of chromatin silencing at telomere    The maintenance of chromatin in a transcriptionally silent state such as heterochromatin at the telomere.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031081    nuclear pore distribution    Any process that establishes the spatial arrangement of nuclear pores within the nuclear envelope.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000973    posttranscriptional 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 even after transcription has been repressed.
    GO:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    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:0000055    ribosomal large subunit export from nucleus    The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
    GO:0034398    telomere tethering at nuclear periphery    The process in which a telomere is maintained in a specific location at the nuclear periphery.
    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.
cellular component
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        NU120_YEAST | P357293f7f 3h7n 4xmm 4xmn

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3HXR)