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(-) Description

Title :  KARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS
 
Authors :  E. Conti, M. Uy, L. Leighton, G. Blobel, J. Kuriyan
Date :  14 Jul 98  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Protein Transport, Nls Nuclear Import, Armadillo Repeat Containing Protein, Complex (Protein Transport/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Conti, M. Uy, L. Leighton, G. Blobel, J. Kuriyan
Crystallographic Analysis Of The Recognition Of A Nuclear Localization Signal By The Nuclear Import Factor Karyopherin Alpha.
Cell(Cambridge, Mass. ) V. 94 193 1998
PubMed-ID: 9695948  |  Reference-DOI: 10.1016/S0092-8674(00)81419-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KARYOPHERIN ALPHA
    Cellular Location: CYTOPLASMIC/NUCLEAR
    Cell Line: BL21
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PPROEX-HTB
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: ARMADILLO DOMAIN
    Gene: SRP1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Strain: W303
    Synonym: IMPORTIN ALPHA, SRP1P
 
Molecule 2 - LARGE T ANTIGEN
    Chains: C, E
    Engineered: YES
    Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL)
    Other Details: NLS PEPTIDE AT THE LARGER (FUNCTIONAL) BINDING SITE
 
Molecule 3 - LARGE T ANTIGEN
    Chains: D, F
    Engineered: YES
    Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL)
    Other Details: NLS PEPTIDE AT THE SMALLER BINDING SITE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BK6)

(-) Sites  (0, 0)

(no "Site" information available for 1BK6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BK6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BK6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BK6)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARM_REPEATPS50176 Armadillo/plakoglobin ARM repeat profile.IMA1_YEAST130-173
 
341-375
 		  4A:130-173
B:130-173
A:341-375
B:341-375
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARM_REPEATPS50176 Armadillo/plakoglobin ARM repeat profile.IMA1_YEAST130-173
 
341-375
 		  2A:130-173
-
A:341-375
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARM_REPEATPS50176 Armadillo/plakoglobin ARM repeat profile.IMA1_YEAST130-173
 
341-375
 		  2-
B:130-173
-
B:341-375

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL189W1YNL189W.1XIV:284261-2858891629IMA1_YEAST1-5425422A:89-510
B:89-510		422
422

(-) 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_YEAST | Q02821 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:422
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  
           IMA1_YEAST    89 LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPPLVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEVTLDALENILKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG 510
               SCOP domains d1bk6a_ A: Karyopherin alpha                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1bk6A00 A:89-510 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------ARM_REPEAT  PDB: A:130-173 UniProt: 130-173 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------ARM_REPEAT  PDB: A:341-375         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:89-510 UniProt: 1-542 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1bk6 A  89 LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPPLVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEVTLDALENIIKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG 510
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  


Chain B from PDB  Type:PROTEIN  Length:422
 aligned with IMA1_YEAST | Q02821 from UniProtKB/Swiss-Prot  Length:542

    Alignment length:422
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  
           IMA1_YEAST    89 LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPPLVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEVTLDALENILKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG 510
               SCOP domains d1bk6b_ B: Karyopherin alpha                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1bk6B00 B:89-510 Leucine-rich Repeat Variant                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------ARM_REPEAT  PDB: B:130-173 UniProt: 130-173 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------ARM_REPEAT  PDB: B:341-375         --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:89-510 UniProt: 1-542 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1bk6 B  89 LPQMTQQLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAWALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQCNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIYSMDTETLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNITAGNTEQIQAVIDANLIPPLVKLLEVAEYKTKKEACWAISNASSGGLQRPDIIRYLVSQGCIKPLCDLLEIADNRIIEVTLDALENIIKMGEADKEARGLNINENADFIEKAGGMEKIFNCQQNENDKIYEKAYKIIETYFG 510
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508  


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
                 1bk6 C 127 KKKRKV 132


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1bk6 D 127 AKKAA 131


Chain E 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
                 1bk6 E 127 KKKRKV 132


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1bk6 F 127 AKKAA 131
   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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BK6)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IMA1_YEAST | Q02821)
molecular function
    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:0031144    proteasome localization    Any process in which the proteasome is transported to, or maintained in, a specific location.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    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:0000176    nuclear exosome (RNase complex)    A ribonuclease complex that has 3-prime to 5-prime processive and distributive hydrolytic exoribonuclease activity and endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IMA1_YEAST | Q02821: 1bk5 1ee4 1ee5 1un0 1wa5 2c1t 4pvz 4xzr 5h2w 5h2x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BK6)