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(-) Description

Title :  CRYSTAL STRUCTURE OF CRM1 INHIBITOR LEPTOMYCIN B IN COMPLEX WITH CRM1(K548A)-RAN-RANBP1
 
Authors :  Q. Sun, Y. M. Chook
Date :  27 Sep 12  (Deposition) - 09 Jan 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Heat Repeat, Nuclear Export, Ran-Ranbp1, Lmb, Leptomycin B, Protein Transport-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Sun, Y. P. Carrasco, Y. Hu, X. Guo, H. Mirzaei, J. Macmillan, Y. M. Chook
Nuclear Export Inhibition Through Covalent Conjugation And Hydrolysis Of Leptomycin B By Crm1.
Proc. Natl. Acad. Sci. Usa V. 110 1303 2013
PubMed-ID: 23297231  |  Reference-DOI: 10.1073/PNAS.1217203110

(-) Compounds

Molecule 1 - GTP-BINDING NUCLEAR PROTEIN RAN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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
    Fragment: RANDB1 (UNP RESIDUES 62-201)
    Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CHROMOSOME STABILITY PROTEIN 20, PERINUCLEAR ARRAY-LOCALIZED PROTEIN, RAN-BINDING PROTEIN 1, RANBP1
 
Molecule 3 - EXPORTIN-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SEE REMARK 999
    Gene: CRM1, KAP124, XPO1, YGR218W, G8514
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CRM1, CHROMOSOME REGION MAINTENANCE PROTEIN 1, KARYOPHERIN- 124

 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
4GOL3Ligand/IonGLYCEROL
5LMB1Ligand/IonLEPTOMYCIN B, BOUND FORM
6MG2Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , 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:417 , HOH A:419 , HOH A:488 , HOH A:560 , HOH A:586 , HOH A:587BINDING SITE FOR RESIDUE GNP A 301
02AC2SOFTWARETHR A:24 , THR A:42 , GNP A:301 , HOH A:586 , HOH A:587BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREGLU A:198 , HOH A:597BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREASN A:103 , ASP A:107 , HOH A:462BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWARELYS C:525 , ILE C:532 , CYS C:539 , ARG C:543 , ILE C:555 , HIS C:569 , THR C:575 , LYS C:579 , HOH C:1821 , HOH C:1970 , HOH C:1984 , HOH C:2092 , HOH C:2124BINDING SITE FOR RESIDUE LMB C 1101
06AC6SOFTWAREHIS A:105 , VAL A:109 , ARG A:110 , LYS A:142 , GLU C:164 , ARG C:219BINDING SITE FOR RESIDUE GOL C 1102
07AC7SOFTWARELEU C:842 , ASN C:846 , TRP C:891 , HOH C:1527 , HOH C:1890 , HOH C:2020BINDING SITE FOR RESIDUE GOL C 1103
08AC8SOFTWAREARG C:327 , GLU C:331 , ASP C:372 , LYS C:416 , HOH C:1844BINDING SITE FOR RESIDUE EDO C 1104
09AC9SOFTWARETHR C:1007 , SER C:1008 , GLU C:1009 , HOH C:2118BINDING SITE FOR RESIDUE CL C 1105
10BC1SOFTWARELYS C:605 , CYS C:606 , LYS C:607 , TYR C:608BINDING SITE FOR RESIDUE CL C 1106
11BC2SOFTWAREPRO C:61 , GLN C:62BINDING SITE FOR RESIDUE CL C 1107
12BC3SOFTWAREHOH C:2078 , HOH C:2117 , HOH C:2128BINDING SITE FOR RESIDUE MG C 1108

(-) SS Bonds  (0, 0)

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

(-) 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 4HAW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HAW)

(-) 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:196
                                                                                                                                                                                                                                     
               SCOP domains d4hawa_ A: Ran                                                                                                                                                                                       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................hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4haw A    9 VQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEHDLEVAQTTALPDEDDDL  216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      |200       210      
                                                                                                                                                                                                          185|                  
                                                                                                                                                                                                           198                  


Chain B from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                    
               SCOP domains d4hawb_ B: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeeeeeeeee....eeeeeeeeeeeeeee.....eeeeee......eeeeee...............eeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                4haw B   63 IHFEPVVKTMEEDEEVLYKVRAKLFRFDKDAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKK  200
                                  ||79        89        99       109       119       129       139       149       159       169       179       189       199 
                                 69|                                                                                                                           
                                  77                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:1012
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4haw C   -1 GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLDLCVKKRGKDNAAVVASDIMYVVGQYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTALDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFA 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|      700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050  
                                                                                                                                                                                                                                                                                                                                                                                                                   376|                                                                                                                                                                                                                                                                            685|                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                    414                                                                                                                                                                                                                                                                             691
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (82, 96)

Asymmetric/Biological Unit(hide GO term definitions)

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  4haw
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  RAN_HUMAN | P62826
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  XPO1_YEAST | P30822
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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 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4ol0 4wvf 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
        XPO1_YEAST | P30822: 3m1i 3vyc 3wyf 3wyg 4gmx 4gpt 4hat 4hau 4hav 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 5dh9 5dha 5dhf 5di9 5dif 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uwr 5uws 5uwt 5uwu 5uww
        YRB1_YEAST | P41920: 3m1i 4gmx 4gpt 4hat 4hau 4hav 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4wvf 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 4gpt 4hat 4hau 4hav 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4