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(-) Description

Title :  CRYSTAL STRUCTURE OF CLOSED DIMER OF HUMAN IMPORTIN-ALPHA1 (RCH1)
 
Authors :  H. Miyatake, A. Sanjoh, G. Matsuda, Y. Tatsumi, N. Dohmae, Y. Aida
Date :  17 Jan 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Arm Repeat, All Alpha Protein, Armadillo Repeat, Closed Dimer, Nuclear Transport, Importin-Beta, Nls-Carring Proteins, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Miyatake
Crystal Structure Of Closed Dimer Of Human Importin-Alpha1 (Rch1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - IMPORTIN SUBUNIT ALPHA-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 75-497
    GeneKPNA2, RCH1, SRP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRCH1, KARYOPHERIN SUBUNIT ALPHA-2, RAG COHORT PROTEIN 1, SRP1-ALPHA

 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  (1, 17)

Asymmetric Unit (1, 17)
No.NameCountTypeFull Name
1PEG17Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1PEG6Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:456BINDING SITE FOR RESIDUE PEG A 501
02AC2SOFTWAREGLN A:367 , VAL A:410BINDING SITE FOR RESIDUE PEG A 502
03AC3SOFTWARELYS A:388 , ALA A:389 , PHE A:391 , GLN A:394BINDING SITE FOR RESIDUE PEG A 503
04AC4SOFTWAREARG A:227 , PEG A:505 , PHE B:391BINDING SITE FOR RESIDUE PEG A 504
05AC5SOFTWAREGLY A:224 , PEG A:504 , HOH A:684 , PHE B:391 , THR B:430 , ALA B:431 , LYS B:432 , HOH B:695BINDING SITE FOR RESIDUE PEG A 505
06AC6SOFTWAREGLU A:306BINDING SITE FOR RESIDUE PEG A 506
07AC7SOFTWAREARG A:238 , TRP A:273 , TYR A:277BINDING SITE FOR RESIDUE PEG A 508
08AC8SOFTWAREASN A:241 , SER B:152 , PEG B:503BINDING SITE FOR RESIDUE PEG A 509
09AC9SOFTWAREPHE A:391 , LYS A:432 , ARG B:227BINDING SITE FOR RESIDUE PEG A 510
10BC1SOFTWARELYS A:353 , GLU A:354 , TRP A:357 , GLU A:396BINDING SITE FOR RESIDUE PEG A 511
11BC2SOFTWAREARG B:315 , GLU B:396BINDING SITE FOR RESIDUE PEG B 501
12BC3SOFTWARESER A:152 , LYS B:240BINDING SITE FOR RESIDUE PEG B 502
13BC4SOFTWARELYS A:240 , PEG A:509 , SER B:149 , GLY B:150 , SER B:152BINDING SITE FOR RESIDUE PEG B 503
14BC5SOFTWAREVAL B:414 , GLU B:456 , LYS B:459BINDING SITE FOR RESIDUE PEG B 504
15BC6SOFTWAREGLN B:371BINDING SITE FOR RESIDUE PEG B 505
16BC7SOFTWAREVAL B:330BINDING SITE FOR RESIDUE PEG B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:108 -Gln A:109
2Asn A:241 -Pro A:242
3Asn B:241 -Pro B:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067625A157VIMA1_HUMANPolymorphism17850032A/BA157V
2UniProtVAR_013137P165RIMA1_HUMANPolymorphism11545989A/BP165R
3UniProtVAR_067626G365SIMA1_HUMANPolymorphism1059558A/BG365S
4UniProtVAR_014453T430PIMA1_HUMANPolymorphism1059538A/BT430P
5UniProtVAR_067627K453NIMA1_HUMANPolymorphism17850031A/BK453N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067625A157VIMA1_HUMANPolymorphism17850032AA157V
2UniProtVAR_013137P165RIMA1_HUMANPolymorphism11545989AP165R
3UniProtVAR_067626G365SIMA1_HUMANPolymorphism1059558AG365S
4UniProtVAR_014453T430PIMA1_HUMANPolymorphism1059538AT430P
5UniProtVAR_067627K453NIMA1_HUMANPolymorphism17850031AK453N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067625A157VIMA1_HUMANPolymorphism17850032BA157V
2UniProtVAR_013137P165RIMA1_HUMANPolymorphism11545989BP165R
3UniProtVAR_067626G365SIMA1_HUMANPolymorphism1059558BG365S
4UniProtVAR_014453T430PIMA1_HUMANPolymorphism1059538BT430P
5UniProtVAR_067627K453NIMA1_HUMANPolymorphism17850031BK453N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 14)

Asymmetric Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003304591ENSE00001673356chr17:66031848-66031956109IMA1_HUMAN-00--
1.2ENST000003304592ENSE00002150216chr17:66033226-6603332398IMA1_HUMAN1-25250--
1.3ENST000003304593ENSE00001697155chr17:66033474-66033611138IMA1_HUMAN26-71460--
1.4ENST000003304594ENSE00001771132chr17:66036794-6603688289IMA1_HUMAN72-101302A:75-101
B:75-101
27
27
1.5ENST000003304595ENSE00001684697chr17:66038201-66038469269IMA1_HUMAN101-191912A:101-191
B:101-191
91
91
1.6ENST000003304596ENSE00001643282chr17:66039021-6603911595IMA1_HUMAN191-222322A:191-222
B:191-222
32
32
1.7ENST000003304597ENSE00001723038chr17:66039216-66039479264IMA1_HUMAN223-310882A:223-310
B:223-310
88
88
1.8ENST000003304598ENSE00001716874chr17:66039954-66040187234IMA1_HUMAN311-388782A:311-388
B:311-388
78
78
1.9ENST000003304599ENSE00001712528chr17:66040437-66040619183IMA1_HUMAN389-449612A:389-449
B:389-449
61
61
1.10ENST0000033045910ENSE00001781256chr17:66041888-66042037150IMA1_HUMAN450-499502A:450-496
B:450-497
47
48
1.11ENST0000033045911ENSE00001735149chr17:66042620-66042969350IMA1_HUMAN500-529300--

(-) 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:422
 aligned with IMA1_HUMAN | P52292 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:422
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494  
           IMA1_HUMAN    75 NWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYF 496
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------V-------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------P----------------------N------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:75-101    -----------------------------------------------------------------------------------------Exon 1.6  PDB: A:191-222        Exon 1.7  PDB: A:223-310 UniProt: 223-310                                               Exon 1.8  PDB: A:311-388 UniProt: 311-388                                     Exon 1.9  PDB: A:389-449 UniProt: 389-449                    Exon 1.10  PDB: A:450-496 UniProt: 450-499      Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.5  PDB: A:101-191 UniProt: 101-191                                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3wpt A  75 NWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYF 496
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494  

Chain B from PDB  Type:PROTEIN  Length:423
 aligned with IMA1_HUMAN | P52292 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:423
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494   
           IMA1_HUMAN    75 NWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYFS 497
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------V-------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S----------------------------------------------------------------P----------------------N-------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: B:75-101    -----------------------------------------------------------------------------------------Exon 1.6  PDB: B:191-222        Exon 1.7  PDB: B:223-310 UniProt: 223-310                                               Exon 1.8  PDB: B:311-388 UniProt: 311-388                                     Exon 1.9  PDB: B:389-449 UniProt: 389-449                    Exon 1.10  PDB: B:450-497 UniProt: 450-499       Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.5  PDB: B:101-191 UniProt: 101-191                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3wpt B  75 NWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYFS 497
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494   

   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 3WPT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IMA1_HUMAN | P52292)
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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0019054    modulation by virus of host process    The process in which a virus effects a change in the processes and activities of its host organism.
    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:0000018    regulation of DNA recombination    Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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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 Related Entries

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

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        IMA1_HUMAN | P522921efx 1qgk 1qgr 3fex 3fey 4e4v 4wv6

(-) Related Entries Specified in the PDB File

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