4HB4: CRM1 inhibitor Leptomycin B

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(537DLTVK541/GLCEQ)-Ran-RanBP1. Determined by X-ray diffraction at 2.05 Å resolution. Released 9 Jan 2013.

Method

X-ray diffraction

Resolution

2.05 Å

Organisms

Homo sapiens, Saccharomyces cerevisiae

Chains

3

Atoms

12,016

Mol. weight

159.67 kDa

Ligands

LMB, MG, GNP

Released

9 Jan 2013

Explore 4HB4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HB4 contains 83 α-helices and 16 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 7 β-strands

Molecules and chains

>4HB4_1 GTP-binding nuclear protein Ran (chains A)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

>4HB4_2 Ran-specific GTPase-activating protein 1 (chains B)
DIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDKDAKEWKERGTGDCKFLKNKKTNK
VRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSK
ENADKFKEEFEKAQEINKKA

>4HB4_3 Exportin-1 (chains C)
GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFS
TNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKS
DLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAK
ALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELL
STKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLK
ATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEEREL
FKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREF
VKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSI
SGTMSEDTEKRFVVTVIKDLLGLCEQKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRT
VILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTAD
LQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSET
VKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPK
VRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCM
TTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFL
ELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIF
VSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYL
ANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDK
ENA

Ligands and cofactors

Water and common crystallization additives (EDO, CL, GOL) are not listed.

Primary citation

Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1. Sun, Q., Carrasco, Y.P., Hu, Y. et al. Proc Natl Acad Sci U S A (2013) 110:1303-1308. DOI 10.1073/pnas.1217203110 · PubMed

Related structures

Other PDB entries of the same protein (UniProt P62826 (AlphaFold model), which also has an AlphaFold model), best resolution first:

• 3GJ0 1.48 Å, Crystal structure of human RanGDP
• 7MO5 1.55 Å, Crystal Structure of the ZnF4 of Nucleoporin NUP153 in complex with Ran-GDP
• 7MO1 1.6 Å, Crystal Structure of the ZnF1 of Nucleoporin NUP153 in complex with Ran-GDP
• 5CIQ 1.65 Å, Ran GDP wild type tetragonal crystal form
• 7MO2 1.65 Å, Crystal Structure of the ZnF2 of Nucleoporin NUP153 in complex with Ran-GDP
• 5CIT 1.75 Å, Ran GDP wild type monoclinic crystal form
• 5CIW 1.75 Å, Ran GDP Y39A mutant monoclinic crystal form
• 5CJ2 1.75 Å, Ran GDP Y39A mutant triclinic crystal form
• 1I2M 1.76 Å, Ran-RCC1-SO4 complex
• 4HAT 1.78 Å, Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-RanBP1
• 3GJ3 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF2 complex
• 3GJ5 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF4 complex

Browse structure collections

About this viewer

MolViewer shows 4HB4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.