3PEW: S. cerevisiae Dbp5 L327V

S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3. Determined by X-ray diffraction at 1.5 Å resolution. Released 23 Mar 2011.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,944
Mol. weight: 46.84 kDa
Ligands: ADP, MG, BEF
Released: 23 Mar 2011

Explore 3PEW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3PEW contains 17 α-helices and 18 β-strands across 1 chain. 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: 17 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	101-109	9
α-helix	117-127	11
β-strand	134-137	4	1
α-helix	144-155	12
β-strand	165-168	4	1
α-helix	172-185	14
β-strand	193-196	4	1
β-strand	207	1	2
β-strand	211-214	4	1
α-helix	216-224	9
β-strand	228	1	2
β-strand	235-239	5	1
α-helix	241-246	6
α-helix	250-260	11
α-helix	265	1
β-strand	266-271	6	1
α-helix	276-285	10
β-strand	290-292	3	1
α-helix	296-298	3
β-strand	304-310	7	3
α-helix	316-328	13
β-strand	332-336	5	3
α-helix	340-352	13
β-strand	358-360	3	3
α-helix	366-377	12
β-strand	383-386	4	3
α-helix	388-390	3
β-strand	399-404	6	3
β-strand	409	1	4
β-strand	415	1	4
α-helix	417-424	8
β-strand	434-440	7	3
α-helix	443-455	13
β-strand	462-463	2	3
α-helix	469-480	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase DBP5	A	protein	395	Saccharomyces cerevisiae	P20449 (AlphaFold model)
RNA (5'-r(pupupupupupu)-3')	B	RNA	6

Sequence of entity 1 (A), FASTA

>3PEW_1 ATP-dependent RNA helicase DBP5 (chains A)
GAMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA
FSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQI
NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL
VLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGV
MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITT
NVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFN
ILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLKD

Sequence of entity 2 (B), FASTA

>3PEW_2 RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') (chains B)
UUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	3
BEF	Beryllium trifluoride ion	Be F3	1

Water and common crystallization additives (NO3) are not listed.

Primary citation

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP(6) in mRNA export. Montpetit, B., Thomsen, N.D., Helmke, K.J. et al. Nature (2011) 472:238-242. DOI 10.1038/nature09862 · PubMed

Other PDB entries of the same protein (UniProt P20449 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PEY 1.4 Å, S. cerevisiae Dbp5 bound to RNA and ADP BeF3
3GFP 1.8 Å, Structure of the C-terminal domain of the DEAD-box protein Dbp5
5ELX 1.81 Å, S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3
3PEV 2.5 Å, S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6
3PEU 2.6 Å, S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6
3RRM 2.9 Å, S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp
3RRN 4.0 Å, S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6
2KBE solution structure of amino-terminal domain of Dbp5p
2KBF solution structure of carboxyl-terminal domain of Dbp5p

Browse structure collections

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