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(-) Description

Title :  CRYSTAL STRUCTURE OF KPT276 IN COMPLEX WITH CRM1-RAN-RANBP1
 
Authors :  Q. Sun, Y. Chook
Date :  05 Nov 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Crm1, Inhibitor, Sine, Kpt, Transport Protein-Transport Protein Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Haines, O. Herbin, B. De La Hera, O. G. Vidaurre, G. A. Moy, Q. Sun H. Y. Fung, S. Albrecht, K. Alexandropoulos, D. Mccauley, Y. M. Chook, T. Kuhlmann, G. J. Kidd, S. Shacham, P. Casaccia
Nuclear Export Inhibitors Avert Progression In Preclinical Models Of Inflammatory Demyelination.
Nat. Neurosci. V. 18 511 2015
PubMed-ID: 25706475  |  Reference-DOI: 10.1038/NN.3953

(-) Compounds

Molecule 1 - GTP-BINDING NUCLEAR PROTEIN RAN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RAN, ARA24, OK/SW-CL.81
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24,GTPASE RAN,RAS-LIKE PROTEIN TC4,RAS-RELATED NUCLEAR PROTEIN
 
Molecule 2 - RAN-SPECIFIC GTPASE-ACTIVATING PROTEIN 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: CHROMOSOME STABILITY PROTEIN 20,PERINUCLEAR ARRAY-LOCALIZED PROTEIN,RAN-BINDING PROTEIN 1,RANBP1
 
Molecule 3 - CRM1P
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CRM1, R008_G21866
    Mutation: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 1182966
    Strain: R008

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4GOL4Ligand/IonGLYCEROL
5K761Ligand/Ion(2E)-3-{3-[3,5-BIS(TRIFLUOROMETHYL)PHENYL]-1H-1,2,4-TRIAZOL-1-YL}-1-(3,3-DIFLUOROAZETIDIN-1-YL)PROP-2-EN-1-ONE
6MG1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:18 , GLY A:19 , GLY A:20 , THR A:21 , GLY A:22 , LYS A:23 , THR A:24 , THR A:25 , GLU A:36 , LYS A:37 , LYS A:38 , TYR A:39 , ALA A:41 , THR A:42 , GLY A:68 , GLN A:69 , ASN A:122 , LYS A:123 , ASP A:125 , ILE A:126 , SER A:150 , ALA A:151 , LYS A:152 , MG A:302 , HOH A:424 , HOH A:426 , HOH A:499 , HOH A:579 , HOH A:615 , HOH A:616binding site for residue GNP A 301
02AC2SOFTWARETHR A:24 , THR A:42 , GNP A:301 , HOH A:615 , HOH A:616binding site for residue MG A 302
03AC3SOFTWAREASN A:103 , ASP A:107 , HOH A:470binding site for residue EDO A 303
04AC4SOFTWAREHIS A:139 , ARG A:140 , LEU A:144 , GLN A:145 , HOH A:455 , GLN C:313 , GLU C:355 , GLU C:357 , HOH C:1417binding site for residue GOL A 304
05AC5SOFTWARELEU C:536 , CYS C:539 , VAL C:540 , LYS C:548 , ILE C:555 , MET C:556 , VAL C:559 , THR C:575 , VAL C:576 , LEU C:580 , PHE C:583binding site for residue K76 C 1101
06AC6SOFTWARETRP C:500 , SER C:501 , TRP C:502 , ASN C:547binding site for residue GOL C 1102
07AC7SOFTWARELEU C:842 , ASN C:846 , TRP C:891 , HOH C:1662 , HOH C:2014 , HOH C:2047 , HOH C:2168binding site for residue GOL C 1103
08AC8SOFTWARETYR C:967 , GLN C:988 , SER C:992binding site for residue EDO C 1104
09AC9SOFTWAREGLU C:1009 , HOH C:1325binding site for residue CL C 1105
10AD1SOFTWARELYS C:605 , CYS C:606 , LYS C:607 , TYR C:608binding site for residue CL C 1106
11AD2SOFTWAREPRO C:61 , GLN C:62binding site for residue CL C 1107
12AD3SOFTWAREGLU C:191 , ARG C:227 , GLU C:231 , THR C:232binding site for residue GOL C 1108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WVF)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp C:130 -Pro C:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WVF)

(-) Exons   (0, 0)

(no "Exon" information available for 4WVF)

(-) 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:209
                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..hhhhh.hhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.hhhhhh.eeee.........hhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wvf A    8 QVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL  216
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207         


Chain B from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeeeeeee....eeeeeeeeeeeeeee.....eeeeee......eeeeee...............eeeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wvf B   63 IHFEPVVTMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKK  200
                                  ||80        90       100       110       120       130       140       150       160       170       180       190       200
                                 69|                                                                                                                          
                                  78                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:1017
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wvf C   -1 GSMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLDLCVKKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFA 1052
                                     8        18        28        38        48        58        68        78        88        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       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045       
                                                                                                                                                                                                                                                                                                                                                                                                                   376|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                                    414
   Legend:   → Mismatch (orange background)
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    → 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 4WVF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WVF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WVF)

(-) Gene Ontology  (77, 84)

Asymmetric/Biological Unit(hide GO term definitions)

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  4wvf
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  RAN_HUMAN | P62826
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  YRB1_YEAST | P41920
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAN_HUMAN | P62826: 1i2m 1ibr 1k5d 1k5g 1qbk 1rrp 2mmc 2mmg 2n1b 3ch5 3ea5 3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8 3gjx 3nby 3nbz 3nc0 3nc1 3zjy 4c0q 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4ol0 5ciq 5cit 5ciw 5cj2 5cll 5clq 5dh9 5dha 5dhf 5di9 5dif 5dis 5dlq 5fyq 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uwr 5uws 5uwt 5uwu 5uww
        YRB1_YEAST | P41920: 3m1i 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 5dh9 5dha 5dhf 5di9 5dif 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uwr 5uws 5uwt 5uwu 5uww

(-) Related Entries Specified in the PDB File

4gmx 4GMX CONTAINS THE SAME COMPLEX WITH DIFFERENT SINE INHIBITOR.