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(-) Description

Title :  MOUSE IMPORTIN ALPHA-PEPTM NLS PEPTIDE COMPLEX
 
Authors :  A. A. S. Takeda, B. Kobe, M. R. M. Fontes
Date :  17 Dec 09  (Deposition) - 07 Apr 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Armadillo Repeats, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Y. Yang, A. A. S. Takeda, M. R. M. Fontes, J. M. Harris, D. A. Jans, B. Kobe
Probing The Specificity Of Binding To The Major Nuclear Localization Sequence-Binding Site Of Importin-Alpha Using Oriented Peptide Library Screening.
J. Biol. Chem. V. 285 19935 2010
PubMed-ID: 20406804  |  Reference-DOI: 10.1074/JBC.M109.079574

(-) Compounds

Molecule 1 - IMPORTIN SUBUNIT ALPHA-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NLS BINDING DOMAIN (UNP RESIDUES 71-497)
    Gene: KPNA2, RCH1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: IMPORTIN ALPHA-2, KARYOPHERIN SUBUNIT ALPHA-2, SRP1-ALPHA, RAG COHORT PROTEIN 1, PENDULIN, PORE TARGETING COMPLEX 58 KDA SUBUNIT, PTAC58, IMPORTIN ALPHA P1
 
Molecule 2 - PEPTM
    Chains: B, C
    Engineered: YES
    Other Details: THIS SEQUENCE WAS OBTAINED BY AN ORIENTED PEPTIDE LIBRARY APPROACH TO PROBE THE SPECIFICITY OF THE MAJOR NLS BINDING SITE IN IMPORTIN ALPHA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:88 , ASN A:89 , LEU A:90 , HIS A:261 , ASN A:263 , GLN A:297 , LYS A:300BINDING SITE FOR RESIDUE FLC A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L3Q)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:241 -Pro A:242
2Phe A:496 -Ser A:497

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L3Q)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARM_REPEATPS50176 Armadillo/plakoglobin ARM repeat profile.IMA1_MOUSE162-204
119-162
204-230
251-293
293-335
335-377		  6A:162-204
A:119-162
A:204-230
A:251-293
A:293-335
A:335-377

(-) Exons   (0, 0)

(no "Exon" information available for 3L3Q)

(-) 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:427
 aligned with IMA1_MOUSE | P52293 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:427
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       
           IMA1_MOUSE    71 QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
               SCOP domains d3l3qa_ A: Importin alpha                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3l3qA00 A:71-497 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------ARM_REPEAT  PDB: A:162-204 UniProt: 162-204----------------------------------------------ARM_REPEAT  PDB: A:251-293 UniProt: 251-293-----------------------------------------ARM_REPEAT  PDB: A:335-377 UniProt: 335-377------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ------------------------------------------------ARM_REPEAT  PDB: A:119-162 UniProt: 119-162 -----------------------------------------ARM_REPEAT  PDB: A:204-230 --------------------------------------------------------------ARM_REPEAT  PDB: A:293-335 UniProt: 293-335------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l3q A  71 QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFS 497
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3l3q B   7 PFKKKRREA  15


Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3l3q C  10 KKRREA  15
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3L3Q)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IMA1_MOUSE | P52293)
molecular function
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0008139    nuclear localization sequence binding    Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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  IMA1_MOUSE | P52293
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 Related Entries

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

UniProtKB/Swiss-Prot
        IMA1_MOUSE | P52293: 1ejl 1ejy 1ial 1iq1 1pjm 1pjn 1q1s 1q1t 1y2a 2c1m 2ynr 3btr 3knd 3oqs 3q5u 3rz9 3rzx 3tpm 3tpo 3ukw 3ukx 3uky 3ukz 3ul0 3ul1 3uvu 3ve6 3zin 3zio 3zip 3ziq 3zir 4ba3 4htv 4mz5 4mz6 4oih 4u54 4u58 4u5l 4u5n 4u5o 4u5s 4u5u 4u5v 4uaf 4yi0 4zdu 5b56 5ctt 5d5k 5e6q 5ekf 5ekg 5fc8 5hhg 5huw 5huy 5k9s 5klr 5klt 5svz 5wum 5wun 5x8n

(-) Related Entries Specified in the PDB File

1ejl MOUSE IMPORTIN ALPHA - SV40 NLS PEPTIDE COMPLEX
1ejy MOUSE IMPORTIN ALPHA-NUCLEOPLASMIN NLS PEPTIDE COMPLEX
1ial MOUSE IMPORTIN ALPHA
1iq1 CRYSTAL STRUCTURE OF THE IMPORTIN-ALPHA(44-54)-IMPORTIN- ALPHA(70-529) COMPLEX
1pjm MOUSE IMPORTIN ALPHA-BIPARTITE NLS FROM HUMAN RETINOBLASTOMA PROTEIN COMPLEX
1pjn MOUSE IMPORTIN ALPHA - N1N2 NLS PEPTIDE COMPLEX
1q1s MOUSE IMPORTIN ALPHA- PHOSPHORYLATED SV40 CN PEPTIDE COMPLEX
1q1t MOUSE IMPORTIN ALPHA - NON-PHOSPHORYLATED SV40 CN PEPTIDE COMPLEX