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(-) Description

Title :  CRYSTRAL STRUCTURE OF THE NUCLEOPORIN NIC96
 
Authors :  N. Schrader, P. Stelter, D. Flemming, K. Kunze, E. Hurt, I. R. Vetter
Date :  01 Oct 07  (Deposition) - 29 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Alpha-Superhelix, Mrna Transport, Nuclear Pore Complex, Nucleus, Protein Transport, Translocation, Transport, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schrader, P. Stelter, D. Flemming, R. Kunze, E. Hurt, I. R. Vetter
Structural Basis Of The Nic96 Subcomplex Organization In Th Nuclear Pore Channel.
Mol. Cell V. 29 46 2008
PubMed-ID: 18206968  |  Reference-DOI: 10.1016/J.MOLCEL.2007.10.022

(-) Compounds

Molecule 1 - NUCLEOPORIN NIC96
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3) RIL CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 189-839
    Gene: NIC96
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: NUCLEAR PORE PROTEIN NIC96, 96 KDA NUCLEOPORIN-INTERACTING COMPONENT

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2RFO)

(-) Sites  (0, 0)

(no "Site" information available for 2RFO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RFO)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFR002W1YFR002W.1VI:150011-1525302520NIC96_YEAST1-8398392A:204-835 (gaps)
B:206-833 (gaps)		632
628

(-) 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:612
 aligned with NIC96_YEAST | P34077 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:632
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833  
          NIC96_YEAST   204 ENNILREKFENYARIVFQFNNSRQANGNFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFKIDSSTRLTKKPKRDIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILNESKYQSSTKGQQIDSLKNVARQCMIYAGMIQYRMPRETYSTLINI 835
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...............ee..eehhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhh........hhhhhhhhhhhh.............hhhhhhhhhhhh................hhhhhhhhhhh.hhhh...hhhhhhh...............hhhhhhhhhhhhhh....-----------.....hhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhheee.....eeehhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh........hhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhh....---------...hhhhhhhhhhhhhhhhh..........hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:204-835 (gaps) UniProt: 1-839 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                 2rfo A 204 ENNILREKFENYARIVFQFNNSRQANGNFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFK-----------KRDIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILN---------GQQIDSLKNVARQCMIYAGMIQYRMPRETYSTLINI 835
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513   |     -     | 533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783      |  -      |803       813       823       833  
                                                                                                                                                                                                                                                                                                                                                   517         529                                                                                                                                                                                                                                                                  790       800                                   


Chain B from PDB  Type:PROTEIN  Length:609
 aligned with NIC96_YEAST | P34077 from UniProtKB/Swiss-Prot  Length:839

    Alignment length:628
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825        
          NIC96_YEAST   206 NILREKFENYARIVFQFNNSRQANGNFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLFKIDSSTRLTKKPKRDIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILNESKYQSSTKGQQIDSLKNVARQCMIYAGMIQYRMPRETYSTLI 833
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Nic96-2rfoB01 B:206-825                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     -------- Pfam domains (1)
           Pfam domains (2) Nic96-2rfoB02 B:206-825                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     -------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh...............ee..eehhhhhhhhhh...hhhhhhhhhhhh.......hhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhh...............hhhhhhhhhh.................hhhhhhhhhhh.hhhh...hhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhh...------------.....hhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhh.eee.....eee.hhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..-------..hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:206-833 (gaps) UniProt: 1-839 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          Transcript 1
                 2rfo B 206 NILREKFENYARIVFQFNNSRQANGNFDIANEFISILSSANGTRNAQLLESWKILESMKSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNEGLATNVNKIKSFIDTKLKKADKSWKISNLTVINGVPIWALIFYLLRAGLIKEALQVLVENKANIKKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIKSSLDGDPYRLAVYKLIGRCDLSRKNIPAVTLSIEDWLWMHLMLIKEKDAENDPVYERYSLEDFQNIIISYGPSRFSNYYLQTLLLSGLYGLAIDYTYTFSEMDAVHLAIGLASLKLF------------KRDIRFANILANYTKSFRYSDPRVAVEYLVLITLNEGPTDVELCHEALRELVLETKEFTVLLGKIGRDGARIPGVIEERQPLLHVRDEKEFLHTITEQAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNPVLLARRMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMELLDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNMIHILN-------TKGQQIDSLKNVARQCMIYAGMIQYRMPRETYSTLI 833
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515|        -   |   535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785    |    -  |    805       815       825        
                                                                                                                                                                                                                                                                                                                                                516          529                                                                                                                                                                                                                                                                  790     798
   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 2RFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Nic96] (2)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NIC96_YEAST | P34077)
molecular function
    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: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:0051292    nuclear pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.
    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: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: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: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:0044612    nuclear pore linkers    A substructure of the nuclear pore complex (NPC) that serves to connect members of the central transport channel (composed of FG-nucleoporins) to the core scaffold (composed of the inner and outer NPC rings). In S. cerevisiae, the linkers are Nic96p and Nup82p. In vertebrates, they are Nup93 and Nup88. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. Both linkers can be isolated in association with specific FG-nucleoporins, complexes that are sometimes referred to as the Nic96 complex (Nic96p-Nsp1p-Nup49p-Nup57p) and the Nup82 complex (Nup82p-Nup116p-Nup159p-Gle2p).
    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
        NIC96_YEAST | P34077: 2qx5

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