2KBF: Carboxyl-terminal domain of Dbp5p

solution structure of carboxyl-terminal domain of Dbp5p. Determined by solution NMR. Released 13 Oct 2009.

Method: Solution NMR
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 1,479
Mol. weight: 21.05 kDa
Released: 13 Oct 2009

Explore 2KBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KBF contains 7 α-helices and 7 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	307-309	3	1
α-helix	314-325	12
β-strand	333-336	4	1
α-helix	340-352	13
β-strand	358-360	3	1
α-helix	366-377	12
β-strand	383-386	4	1
α-helix	392-394	3
β-strand	402-404	3	1
α-helix	417-425	9
β-strand	436-439	4	1
α-helix	443-456	14
β-strand	462-464	3	1
α-helix	470-478	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase DBP5	A	protein	187	Saccharomyces cerevisiae	P20449 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KBF_1 ATP-dependent RNA helicase DBP5 (chains A)
TNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSEGH
EVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQA
DPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKI
VKKVLKD

Primary citation

Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides. Fan, J.S., Cheng, Z., Zhang, J. et al. J Mol Biol (2009) 388:1-10. DOI 10.1016/j.jmb.2009.03.004 · 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
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

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