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(-) Description

Title :  CRYSTAL STRUCTURE OF CRM1 INHIBITOR LEPTOMYCIN B IN COMPLEX WITH CRM1(K548E,K579Q)-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 :  2.30
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  (5, 11)

Asymmetric/Biological Unit (5, 11)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
4LMB1Ligand/IonLEPTOMYCIN B, BOUND FORM
5MG1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
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 , PHE A:35 , GLU A:36 , LYS A:37 , TYR A:39 , ALA A:41 , THR A:42 , GLY A:68 , 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:461 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE GNP A 301
02AC2SOFTWARETHR A:24 , THR A:42 , GNP A:301 , HOH A:500 , HOH A:501BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREASP A:107 , HOH A:453BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWARELYS C:525 , CYS C:539 , VAL C:540 , ARG C:543 , ILE C:555 , HIS C:569 , PHE C:572BINDING SITE FOR RESIDUE LMB C 1101
05AC5SOFTWAREARG C:327 , GLU C:331 , ASP C:372 , GLU C:376BINDING SITE FOR RESIDUE EDO C 1102
06AC6SOFTWARETYR C:967 , GLN C:988 , SER C:992 , THR C:1019BINDING SITE FOR RESIDUE EDO C 1103
07AC7SOFTWARELYS A:167 , HOH A:487 , ALA C:304 , ASN C:305 , GLY C:306 , ASN C:307 , ASP C:308 , GLN C:309 , SER C:310BINDING SITE FOR RESIDUE EDO C 1104
08AC8SOFTWAREGLY C:722 , VAL C:786 , HOH C:1696BINDING SITE FOR RESIDUE EDO C 1105
09AC9SOFTWARESER C:520 , THR C:1007BINDING SITE FOR RESIDUE CL C 1106
10BC1SOFTWARELYS C:605 , CYS C:606 , TYR C:608BINDING SITE FOR RESIDUE CL C 1107
11BC2SOFTWAREPRO C:61 , GLN C:62BINDING SITE FOR RESIDUE CL C 1108

(-) SS Bonds  (0, 0)

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

(-) 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 4HAY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HAY)

(-) 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:200
                                                                                                                                                                                                                                         
               SCOP domains d4haya_ 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.................hhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4hay A    9 VQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEAQYEHDLEVAQTTALPDEDDDL  216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       196       206       216
                                                                                                                                                                                                           186|                     
                                                                                                                                                                                                            195                     


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains d4hayb_ B: automated matches                                                                                              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
                4hay B   80 EEDEEVLYKVRAKLFRFDKDAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKK  200
                                    89        99       109       119       129       139       149       159       169       179       189       199 


Chain C from PDB  Type:PROTEIN  Length:1014
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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..hhhhhhhhhhhhhhhhhh.........eee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4hay C   -1 GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLDLCVKKRGKDNEAVVASDIMYVVGQYPRFLKAHWNFLRTVILQLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFA 1052
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     ||209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369      |416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686 ||    697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977|      988       998      1008      1018      1028      1038      1048    
                                                                                                                                                                                                                                       204|                                                                                                                                                                       376|                                                                                                                                                                                                                                                                               688|                                                                                                                                                                                                                                                                                            977|                                                                         
                                                                                                                                                                                                                                        206                                                                                                                                                                        414                                                                                                                                                                                                                                                                                690                                                                                                                                                                                                                                                                                             979
   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 4HAY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (82, 96)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hay
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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 4haw 4hax 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 4haw 4hax 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 4haw 4hax 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 4haw 4hax 4haz 4hb0 4hb2 4hb3 4hb4