5DIF: CPEB4 NES Peptide

Crystal Structure of CPEB4 NES Peptide in complex with CRM1-Ran-RanBP1. Determined by X-ray diffraction at 2.09 Å resolution. Released 16 Sept 2015.

Method: X-ray diffraction
Resolution: 2.09 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 11,972
Mol. weight: 164.1 kDa
Ligands: MG, GNP
Released: 16 Sept 2015

Explore 5DIF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DIF contains 87 α-helices and 14 β-strands across 4 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	10-16	7	1
α-helix	23-32	10
β-strand	45-55	11	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	182-187	6
α-helix	191-193	3
α-helix	194-205	12
α-helix	208-209	2

Chain B: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
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: 71 helices, 0 β-strands

Element	Residues	Length
α-helix	0-5	6
α-helix	10-11	2
α-helix	13-25	13
α-helix	28-43	16
α-helix	47-50	4
α-helix	51-57	7
α-helix	61-77	17
α-helix	79-81	3
α-helix	84-103	20
α-helix	105-110	6
α-helix	112-129	18
α-helix	137-145	9
α-helix	149-163	15
α-helix	164-168	5
α-helix	176-188	13
α-helix	190-203	14
α-helix	207-220	14
α-helix	227-230	4
α-helix	234-239	6
α-helix	241-244	4
α-helix	246-259	14
α-helix	269-285	17
α-helix	286-290	5
α-helix	297-303	7
α-helix	308-326	19
α-helix	328-331	4
α-helix	334-336	3
α-helix	337-350	14
α-helix	356-375	20
α-helix	417-420	4
α-helix	421-433	13
α-helix	435-437	3
α-helix	462-478	17
α-helix	480-495	16
α-helix	502-514	13
α-helix	521-541	21
α-helix	545-561	17
α-helix	563-568	6
α-helix	570-583	14
α-helix	591-606	16
α-helix	608-611	4
α-helix	613-614	2
α-helix	621-627	7
α-helix	629-632	4
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	952-966	15
α-helix	987-1002	16
α-helix	1008-1020	13
α-helix	1025-1038	14
α-helix	1046-1050	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	384-391	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding nuclear protein Ran	A	protein	237	Homo sapiens	P62826 (AlphaFold model)
Ran-specific GTPase-activating protein 1	B	protein	143	Saccharomyces cerevisiae	P41920 (AlphaFold model)
Exportin-1	C	protein	1024	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P30822 (AlphaFold model)
Cytoplasmic polyadenylation element-binding protein 4	D	protein	19	Homo sapiens	Q17RY0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5DIF_1 GTP-binding nuclear protein Ran (chains A)
METGSSHHHHHHSSGLPRGSHMAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKY
VATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYK
NVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEK
PFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 2 (B), FASTA

>5DIF_2 Ran-specific GTPase-activating protein 1 (chains B)
GGSDIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKK
TNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRF
GSKENADKFKEEFEKAQEINKKA

Sequence of entity 3 (C), FASTA

>5DIF_3 Exportin-1 (chains C)
GGSMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQKADQILQF
STNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINK
SDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQA
KALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILEL
LSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADL
KATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERE
LFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEDLVVENDEGEIVRE
FVKESDTIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGS
ISGTMSEDTEKRFVVTVIKDLLGLCEQKRGKDNKAVVASDIMYVVGQYPRFLKAHWNFLR
TVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTA
DLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSE
TVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISAQVAAEGLIATKTP
KVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNC
MTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAF
LELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFI
FVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQY
LANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAED
KENA

Sequence of entity 4 (D), FASTA

>5DIF_4 Cytoplasmic polyadenylation element-binding protein 4 (chains D)
GGSYRTFDMHSLESSLIDI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1

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

Primary citation

Structural determinants of nuclear export signal orientation in binding to exportin CRM1. Fung, H.Y., Fu, S.C., Brautigam, C.A. et al. Elife (2015) 4. DOI 10.7554/eLife.10034 · 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
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

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