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(-) Description

Title :  CRYSTAL STRUCTURE OF NTF2 M118E MUTANT
 
Authors :  C. Chaillan-Huntington, P. J. Butler, J. A. Huntington, D. Akin, C. Feldherr, M. Stewart
Date :  01 Jun 01  (Deposition) - 13 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ntf2, Transport, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Chaillan-Huntington, P. J. Butler, J. A. Huntington, D. Akin, C. Feldherr, M. Stewart
Ntf2 Monomer-Dimer Equilibrium.
J. Mol. Biol. V. 314 465 2001
PubMed-ID: 11846560  |  Reference-DOI: 10.1006/JMBI.2001.5136
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR TRANSPORT FACTOR 2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1JB5)

(-) Sites  (0, 0)

(no "Site" information available for 1JB5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JB5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JB5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JB5)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NTF2_DOMAINPS50177 Nuclear transport factor 2 domain profile.NTF2_RAT10-121
 
  2A:10-121
B:10-121

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000256081ENSRNOE00000363046chr19:35697564-3569759633NTF2_RAT-00--
1.2ENSRNOT000000256082ENSRNOE00000230100chr19:35711999-35712125127NTF2_RAT1-33332A:4-33
B:4-33
30
30
1.3ENSRNOT000000256083ENSRNOE00000230088chr19:35714265-3571433672NTF2_RAT34-57242A:34-57
B:34-57
24
24
1.4ENSRNOT000000256084ENSRNOE00000230084chr19:35714421-3571451999NTF2_RAT58-90332A:58-90
B:58-90
33
33
1.5ENSRNOT000000256085ENSRNOE00000183551chr19:35717241-357188361596NTF2_RAT91-127372A:91-126
B:91-126
36
36

(-) 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:123
 aligned with NTF2_RAT | P61972 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:123
                                    13        23        33        43        53        63        73        83        93       103       113       123   
             NTF2_RAT     4 KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNF 126
               SCOP domains d1jb5a_ A: Nuclear transport factor-2 (NTF2)                                                                                SCOP domains
               CATH domains 1jb5A00 A:4-126  [code=3.10.450.50, no name defined]                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeehhhhhhhhhh......eeeeeeeeeeee.....eeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------NTF2_DOMAIN  PDB: A:10-121 UniProt: 10-121                                                                      ----- PROSITE
               Transcript 1 Exon 1.2  PDB: A:4-33         Exon 1.3  PDB: A:34-57  Exon 1.4  PDB: A:58-90           Exon 1.5  PDB: A:91-126 [INCOMPLETE] Transcript 1
                 1jb5 A   4 KPIWEQIGSSFINHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDEFRLALHNF 126
                                    13        23        33        43        53        63        73        83        93       103       113       123   

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with NTF2_RAT | P61972 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:123
                                    13        23        33        43        53        63        73        83        93       103       113       123   
             NTF2_RAT     4 KPIWEQIGSSFIQHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMFRLALHNF 126
               SCOP domains d1jb5b_ B: Nuclear transport factor-2 (NTF2)                                                                                SCOP domains
               CATH domains 1jb5B00 B:4-126  [code=3.10.450.50, no name defined]                                                                        CATH domains
           Pfam domains (1) ------NTF2-1jb5B01 B:10-121                                                                                           ----- Pfam domains (1)
           Pfam domains (2) ------NTF2-1jb5B02 B:10-121                                                                                           ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeehhhhhhhhhhhh....eeeeeeeeeeee.....eeeeeeeeeee.....eeeeeeeeeee....eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------NTF2_DOMAIN  PDB: B:10-121 UniProt: 10-121                                                                      ----- PROSITE
               Transcript 1 Exon 1.2  PDB: B:4-33         Exon 1.3  PDB: B:34-57  Exon 1.4  PDB: B:58-90           Exon 1.5  PDB: B:91-126 [INCOMPLETE] Transcript 1
                 1jb5 B   4 KPIWEQIGSSFINHYYQLFDNDRTQLGAIYIDASCLTWEGQQFQGKAAIVEKLSSLPFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDEFRLALHNF 126
                                    13        23        33        43        53        63        73        83        93       103       113       123   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NTF2 (66)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NTF2_RAT | P61972)
molecular function
    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: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).
biological process
    GO:1904046    negative regulation of vascular endothelial growth factor production    Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial growth factor production.
    GO:0042307    positive regulation of protein import into nucleus    Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.
    GO:0006611    protein export from nucleus    The directed movement of a protein from the nucleus into the cytoplasm.
    GO:0000060    protein import into nucleus, translocation    A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope.
    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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005640    nuclear outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NTF2_RAT | P619721a2k 1ar0 1ask 1gy5 1gy6 1jb2 1jb4 1oun 1qma 1u5o 5bxq

(-) Related Entries Specified in the PDB File

1jb2 1JB2 CONTAINS THE SAME PROTEIN M84E MUTANT
1jb4 1JB4 CONTAINS THE SAME PROTEIN M102E MUTANT