5ELX: S. cerevisiae Dbp5

S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3. Determined by X-ray diffraction at 1.81 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Saccharomyces cerevisiae (strain YJM789)
Chains: 2
Atoms: 3,627
Mol. weight: 46.4 kDa
Ligands: MG, BEF, M2A
Released: 24 Feb 2016

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

Secondary structure: helices and β-sheets

5ELX 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	250-258	9
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	314-325	12
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	391	Saccharomyces cerevisiae (strain YJM789)	P20449 (AlphaFold model)
RNA (5'-r(pupupupupupu)-3')	B	RNA	6	Saccharomyces cerevisiae (strain YJM789)

Sequence of entity 1 (A), FASTA

>5ELX_1 ATP-dependent RNA helicase DBP5 (chains A)
AKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL
TMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQINAQ
VIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLF
SATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTI
GSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVL
ARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILS
AIQKYFGDIEMTRVPTDDWDEVEKIVKKVLK

Sequence of entity 2 (B), FASTA

>5ELX_2 RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') (chains B)
UUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
BEF	Beryllium trifluoride ion	Be F3	1
M2A	[(2~{R},3~{R},4~{R},5~{S})-2-(6-aminopurin-9-yl)-4-oxidanyl-5-[[oxidanyl(phosph…	C18 H22 N6 O11 P2	1

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

Primary citation

Pi Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5). Wong, E.V., Cao, W., Voros, J. et al. J Mol Biol (2016) 428:492-508. DOI 10.1016/j.jmb.2015.12.018 · 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
3PEW 1.5 Å, S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3
3GFP 1.8 Å, Structure of the C-terminal domain of the DEAD-box protein Dbp5
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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