4HAT: CRM1 inhibitor Leptomycin B

Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1-Ran-RanBP1. Determined by X-ray diffraction at 1.78 Å resolution. Released 9 Jan 2013.

Method: X-ray diffraction
Resolution: 1.78 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 3
Atoms: 12,628
Mol. weight: 159.84 kDa
Ligands: LMB, MG, GNP
Released: 9 Jan 2013

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

Secondary structure: helices and β-sheets

4HAT contains 84 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

Element	Residues	Length	Sheet
β-strand	10-17	8	1
α-helix	23-32	10
β-strand	45-54	10	1
β-strand	57-66	10	1
α-helix	70-72	3
α-helix	76-80	5
β-strand	85-91	7	1
α-helix	95-99	5
α-helix	101-111	11
β-strand	117-122	6	1
α-helix	133-135	3
α-helix	138-142	5
β-strand	145-148	4	1
α-helix	159-169	11
β-strand	176	1	1
α-helix	178-180	3
α-helix	182-186	5
α-helix	191-193	3
α-helix	194-205	12
α-helix	208-209	2

Chain B: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	83-97	15	2
β-strand	102-116	15	2
β-strand	122-127	6	2
β-strand	134-139	6	2
β-strand	147	1	2
β-strand	155-163	9	2
β-strand	170-178	9	2
α-helix	181-199	19

Chain C: 70 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	0-5	6
α-helix	13-25	13
α-helix	28-43	16
α-helix	47-50	4
α-helix	51-57	7
α-helix	61-78	18
α-helix	79-81	3
α-helix	84-103	20
α-helix	105-110	6
α-helix	112-129	18
α-helix	137-144	8
α-helix	149-163	15
α-helix	164-168	5
α-helix	176-203	28
α-helix	208-220	13
α-helix	227-230	4
α-helix	234-239	6
α-helix	241-244	4
α-helix	246-260	15
α-helix	269-285	17
α-helix	286-290	5
α-helix	297-303	7
α-helix	308-326	19
α-helix	327-330	4
α-helix	334-336	3
α-helix	337-350	14
α-helix	356-373	18
α-helix	417-420	4
α-helix	421-433	13
α-helix	435-438	4
β-strand	443-445	3	3
β-strand	451-453	3	3
α-helix	459-461	3
α-helix	462-478	17
α-helix	480-495	16
α-helix	502-514	13
α-helix	521-541	21
α-helix	545-560	16
α-helix	563-568	6
α-helix	570-583	14
α-helix	589-606	18
α-helix	608-611	4
α-helix	621-627	7
α-helix	629-633	5
α-helix	638-652	15
α-helix	658-668	11
α-helix	670-685	16
α-helix	689-691	3
α-helix	693-713	21
α-helix	714-717	4
α-helix	718-746	29
α-helix	748-752	5
α-helix	754-776	23
α-helix	780-782	3
α-helix	783-788	6
α-helix	789-801	13
α-helix	804-806	3
α-helix	809-822	14
α-helix	823-825	3
α-helix	827-845	19
α-helix	853-869	17
α-helix	872-875	4
α-helix	879-893	15
α-helix	898-918	21
α-helix	922-944	23
α-helix	949-951	3
α-helix	952-967	16
α-helix	977	1
α-helix	987-1002	16
α-helix	1008-1020	13
α-helix	1025-1038	14
α-helix	1046-1050	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A	protein	216	Homo sapiens	P62826 (AlphaFold model)
Ran-specific GTPase-activating protein 1	B	protein	140	Saccharomyces cerevisiae	P41920 (AlphaFold model)
Exportin-1	C	protein	1023	Saccharomyces cerevisiae	P30822 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4HAT_1 GTP-binding nuclear protein Ran (chains A)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B), FASTA

>4HAT_2 Ran-specific GTPase-activating protein 1 (chains B)
DIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDKDAKEWKERGTGDCKFLKNKKTNK
VRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSK
ENADKFKEEFEKAQEINKKA

Sequence of entity 3 (C), FASTA

>4HAT_3 Exportin-1 (chains C)
GAMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQFS
TNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKS
DLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAK
ALHLKNSMSKEFEQIFKLCFQVLEQGASSSLIVATLESLLRYLHWIPYRYIYETNILELL
STKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLK
ATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEEREL
FKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEVLVVENDEGEIVREF
VKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSI
SGTMSEDTEKRFVVTVIKDLLDLCVKKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLRT
VILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTAD
LQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSET
VKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTPK
VRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCM
TTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFL
ELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIF
VSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYL
ANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDK
ENA

Ligands and cofactors

ID	Name	Formula	Copies
LMB	Leptomycin B, bound form	C33 H52 O7	1
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

Water and common crystallization additives (CL, GOL, EDO) 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

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
3GJ3 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF2 complex
3GJ5 1.79 Å, Crystal structure of human RanGDP-Nup153ZnF4 complex
4HB2 1.8 Å, Crystal structure of CRM1-Ran-RanBP1

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