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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KARYOPHERIN KAP121P BOUND TO THE SUMO PROTEASE ULP1P
 
Authors :  J. Kobayashi, Y. Matsuura
Date :  18 Oct 16  (Deposition) - 14 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nuclear Import, Protein Transport-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hirano, J. Kobayashi, Y. Matsuura
Structures Of The Karyopherins Kap121P And Kap60P Bound To The Nuclear Pore-Targeting Domain Of The Sumo Protease Ulp1
J. Mol. Biol. V. 429 249 2017
PubMed-ID: 27939291  |  Reference-DOI: 10.1016/J.JMB.2016.11.029

(-) Compounds

Molecule 1 - IMPORTIN SUBUNIT BETA-3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PSE1, KAP121, YMR308C, YM9952.10C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: KARYOPHERIN SUBUNIT BETA-3,KARYOPHERIN-121,PROTEIN SECRETION ENHANCER 1
 
Molecule 2 - UBIQUITIN-LIKE-SPECIFIC PROTEASE 1
    Chains: B
    EC Number: 3.4.22.68
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-150
    Gene: ULP1, YPL020C, LPB11C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 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 5H2V)

(-) Sites  (0, 0)

(no "Site" information available for 5H2V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H2V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:78 -Pro A:79
2Ser A:440 -Pro A:441
3Gly A:891 -Glu A:892
4Leu A:996 -Pro A:997

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H2V)

(-) Exons   (0, 0)

(no "Exon" information available for 5H2V)

(-) 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:1027
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhh...eeee.eeeeehhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h2v A    3 ALPEEVNRTLLQIVQAFASNQIRSVAEKALSEEWITENNIEYLLTFLAEQAAFSQDTTVAALSAVLFRKLALKAPITHIRKEVLAQIRSSLLKGFLSERADSIRHKLSDAIAECVQDDLPAWPELLQALIESLKSGNPNFRESSFRILTTVPYLITAVDINSILPIFQSGFTDASDNVKIAAVTAFVGYFKQLPKSEWSKLGILLPSLLNSLPRFLDDGKDDALASVFESLIELVELAPKLFKDMFDQIIQFTDMVIKNKDLEPPARTTALELLTVFSENAPQMCKSNQNYGQTLVMVTLIMMTEVSIDDDDAAEWIESDDTDDEEEVTYDHARQALDRVALKLGGEYLAAPLFQYLQQMITSTEWRERFAAMMALSSAAEGCADVLIGEIPKILDMVIPLINDPHPRVQYGCCNVLGQISTDFSPFIQRTAHDRILPALISKLTSECTSRVQTHAAAALVNFSEFASKDILEPYLDSLLTNLLVLLQSNKLYVQEQALTTIAFIAEAAKNKFIKYYDTLMPLLLNVLKVNSVLKGKCMECATLIGFAVGKEKFHEHSQELISILVALQNSDALRSYLEQSWSRICRILGDDFVPLLPIVIPPLLITAKATQDVGLIEEEEAANFQQYPDWDVVKHIAIHTSVLDDKVSAMELLQSYATLLRGQFAVYVKEVMEEIALPSLDFYLHDGVRAAGATLIPILLSCLLAANEELVLLWHKASSKLIGGLMSEPMPEITQVYHNSLVNGIKVMGDNCLSEDQLAAFTKGVSANLTDTYERMQDDEYNEDFTDEDLLDEINKSIAAVLKTTNGHYLKNLENIWPMINTFLLDNEPILVIFALVVIGDLIQYGGEQTASMKNAFIPKVTECLISPDARIRQAASYIIGVCAQYAPSTYADVCIPTLDTLVQIVDGSKLEENRSSTENASAAIAKILYAYDTYTANWFKTLPTITDKEAASFNYQFLSQLIEPIVCAQSNISAVVDSVIQALNERSLEGQTVISSVKKLLGFLDAMAIFNRYPADIMEKVHKWF 1088
                                    12        24        34        44        54        64        74    ||  95       105       115       125       135       145       155       165       175       185       195       205       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|      559       569       579       589||     604       614       624       634       644       654   ||  668       678       688       698       708       718       728      |742       752       762       772       782       792       802       817   ||  833       843       853       863       873       883       893       903       913       923       933       943       955       965       975  ||   992      1002      1012    ||1025      1035      1045|     1058     |1071      1081       
                                             21|                                                     79|                                                                                                                                                                                                                                                                                                                                                                                                                                                                   545|                                     590|                                                           658|                                                                     735|                                                                    811| 821|                                                                                                                        951|                     978|                           1017|                    1045|           1064|                    
                                              24                                                      91                                                                                                                                                                                                                                                                                                                                                                                                                                                                    550                                      596                                                            663                                                                      740                                                                     817  828                                                                                                                         954                      986                            1021                     1049            1068                    


Chain B 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
                5h2v B   51 GIYKK   55
   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 5H2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H2V)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:78 - Pro A:79   [ RasMol ]  
    Gly A:891 - Glu A:892   [ RasMol ]  
    Leu A:996 - Pro A:997   [ RasMol ]  
    Ser A:440 - Pro A:441   [ RasMol ]  
 

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  ULP1_YEAST | Q02724
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  3.4.22.68
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 Related Entries

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

UniProtKB/Swiss-Prot
        IMB3_YEAST | P32337: 3w3t 3w3u 3w3v 3w3w 3w3x 3w3y 3w3z 4zj7
        ULP1_YEAST | Q02724: 1euv 2hkp 2hl8 2hl9 5h2w 5h2x

(-) Related Entries Specified in the PDB File

5h2w 5h2x