7DBG: Yeast CRM1e

Yeast CRM1e (apo) in complex with Ran-RanBP1. Determined by X-ray diffraction at 2.06 Å resolution. Released 29 Sept 2021.

Method

X-ray diffraction

Resolution

2.06 Å

Organisms

Homo sapiens, Saccharomyces cerevisiae

Chains

3

Atoms

11,398

Mol. weight

157.47 kDa

Ligands

MPO, GTP, MG

Released

29 Sept 2021

Explore 7DBG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7DBG contains 84 α-helices and 14 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: 14 helices, 7 β-strands

Molecules and chains

>7DBG_1 GTP-binding nuclear protein Ran (chains A)
MAAQGEPEVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
AAAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

>7DBG_2 YRB1 isoform 1 (chains B)
DIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKKTNK
VRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSK
ENADKFKEEFEKAQEINKKA

>7DBG_3 CRM1 isoform 1 (chains C)
GGSMEGILDFSNDLDIALLDQVVSTFYQGEGVQQKQAQEILTKFQDNPDAWEKVDQILQF
STNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINK
SDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQA
KALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILEL
LSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADL
KATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERE
LFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEIQLYKSEREVLVYL
THLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDL
LGLCEQKRGKDNKAVVARDIMYVVGEYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMA
CDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEE
RSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGA
DFYPQLGHIYYNMLQLYRAVSSMISTQVAAEGLIATKTPKVRGLRTIKKEILKLVETYIS
KARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQ
SVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKH
NNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQ
ALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFL
SALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDKENA

Ligands and cofactors

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

Primary citation

Novel Mechanistic Observations and NES-Binding Groove Features Revealed by the CRM1 Inhibitors Plumbagin and Oridonin. Lei, Y., Li, Y., Tan, Y. et al. J Nat Prod (2021) 84:1478-1488. DOI 10.1021/acs.jnatprod.0c01231 · 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 7DBG 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.