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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF NUCLEAR PORE COMPLEX COMPONENT NUP116 FROM CANDIDA GLABRATA
 
Authors :  P. Sampathkumar, D. Manglicmot, K. Bain, J. Gilmore, T. Gheyi, M. Rout, S. Atwell, D. A. Thompson, J. S. Emtage, S. Wasserman, J. M. Sauder, S. K New York Sgx Research Center For Structural Genomics (Nysgx
Date :  09 Jun 10  (Deposition) - 04 Aug 10  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nuclear Pore Complex, Nup116, Glebs Domain, Structural Genomics, Psi- 2, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, New York Sgx Research Center For Structural Genomics, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Sampathkumar, S. J. Kim, D. Manglicmot, K. T. Bain, J. Gilmore, T. Gheyi, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. D. Franke T. Matsui, H. Tsuruta, S. Atwell, D. A. Thompson, J. S. Emtage, S. R. Wasserman, M. P. Rout, A. Sali, J. M. Sauder, S. C. Almo, S. K. Burle
Atomic Structure Of The Nuclear Pore Complex Targeting Domain Of A Nup116 Homologue From The Yeast, Candida Glabrata.
Proteins V. 80 2110 2012
PubMed-ID: 22544723  |  Reference-DOI: 10.1002/PROT.24102

(-) Compounds

Molecule 1 - NUCLEOPORIN NUP116
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidBC-PSGX3(BC);
MODIFIED PET26B
    Expression System StrainBL21(DE3)-CODON+RIL
    Expression System Taxid469008
    Expression System VectorPET
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN RESIDUES 881-1034
    GeneCAGL0F06171G, NUP116 (GI50287617)
    Organism CommonYEAST
    Organism ScientificCANDIDA GLABRATA
    Organism Taxid5478
    StrainCBS 138
    SynonymSTRAIN CBS138 CHROMOSOME F COMPLETE SEQUENCE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:898 , GLU A:910 , LYS A:913 , VAL A:914 , GLU A:915BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWARETYR A:980 , THR A:1025 , HOH B:141 , TYR B:980 , THR B:1025BINDING SITE FOR RESIDUE GOL B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NF5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:897 -Pro A:898
2Ser B:897 -Pro B:898

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NF5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NF5)

(-) Exons   (0, 0)

(no "Exon" information available for 3NF5)

(-) 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:156
 aligned with Q6FU56_CANGA | Q6FU56 from UniProtKB/TrEMBL  Length:1035

    Alignment length:156
                                   889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      
        Q6FU56_CANGA    880 KLDGIDDLEFVDENYYISPSLDTLATLSKYEIQKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDDLVVFQPMSVLLYNNSTNVPEKGKGLNVRARISCYNCYPLDKSTRKPIKDPNHRIMERYSEKLKKIPHTHFESYDPASGTYCFTVDHALI 1035
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeee.hhhhhhhhhhhhhh.....eeee...eeeee.........hhhhh....eeee..eeee.................eeeee...................hhhhhhhhhhhhh...eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3nf5 A  880 SLDGIDDLEFVDENYYISPSLDTLATLSKYEIQKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDDLVVFQPmSVLLYNNSTNVPEKGKGLNVRARISCYNCYPLDKSTRKPIKDPNHRImERYSEKLKKIPHTHFESYDPASGTYCFTVDHALE 1035
                                   889       899       909       919       929       939       949   |   959       969       979       989       999 |    1009      1019      1029      
                                                                                                   953-MSE                                        1001-MSE                              

Chain B from PDB  Type:PROTEIN  Length:152
 aligned with Q6FU56_CANGA | Q6FU56 from UniProtKB/TrEMBL  Length:1035

    Alignment length:156
                                   889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      
        Q6FU56_CANGA    880 KLDGIDDLEFVDENYYISPSLDTLATLSKYEIQKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDDLVVFQPMSVLLYNNSTNVPEKGKGLNVRARISCYNCYPLDKSTRKPIKDPNHRIMERYSEKLKKIPHTHFESYDPASGTYCFTVDHALI 1035
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------Nucleoporin2-3nf5B01 B:893-1033                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -------------Nucleoporin2-3nf5B02 B:893-1033                                                                                                              -- Pfam domains (2)
         Sec.struct. author ..............eeee.hhhhhh....hhhhhh...eeee...eeeee.........hhhhh....eeee..eeee..----...........eeeee...................hhhhhhhhhhh.....eeeee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3nf5 B  880 SLDGIDDLEFVDENYYISPSLDTLATLSKYEIQKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDDLVVFQPmSVLLYN----VPEKGKGLNVRARISCYNCYPLDKSTRKPIKDPNHRImERYSEKLKKIPHTHFESYDPASGTYCFTVDHALE 1035
                                   889       899       909       919       929       939       949   |   959    |  969       979       989       999 |    1009      1019      1029      
                                                                                                   953-MSE59  964                                 1001-MSE                              

   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 3NF5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NF5)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6FU56_CANGA | Q6FU56)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    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:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    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:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0000055    ribosomal large subunit export from nucleus    The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm.
    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.
cellular component
    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:0044613    nuclear pore central transport channel    The central substructure of the nuclear pore complex (NPC), through which nucleocytoplasmic transport of RNAs, proteins and small molecules occurs. The central transport channel is filled with FG-nucleoporins, which form a selective barrier and provide a series of binding sites for transporter proteins. Characterized S. cerevisiae FG-nucleoporins include Nup159p, Nup145Np, Nup116p, Nup100p, Nsp1p, Nup57p, Nup49p, Nup42p, Nup53p, Nup59p/Asm4p, Nup60p and Nup1. Characterized vertebrate FG-nucleoporins include Nup214, Nup98, Nup62, Nup54, Nup58/45, NLP1, and Nup153.
    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: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).

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