3GFP: C-terminal domain of the DEAD-box protein Dbp5

Structure of the C-terminal domain of the DEAD-box protein Dbp5. Determined by X-ray diffraction at 1.8 Å resolution. Released 1 Sept 2009.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Saccharomyces cerevisiae
Chains: 1
Atoms: 1,575
Mol. weight: 21.37 kDa
Released: 1 Sept 2009

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

Secondary structure: helices and β-sheets

3GFP contains 8 α-helices and 9 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	305-310	6	1
α-helix	316-327	12
β-strand	333-337	5	1
α-helix	340-352	13
β-strand	357-360	4	1
α-helix	366-378	13
β-strand	383-387	5	1
α-helix	396-398	3
β-strand	401-404	4	1
β-strand	409	1	2
β-strand	415	1	2
α-helix	417-424	8
α-helix	432-434	3
β-strand	435-440	6	1
α-helix	443-455	13
β-strand	462-465	4	1
α-helix	469-478	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DEAD box protein 5	A	protein	189	Saccharomyces cerevisiae	P20449 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3GFP_1 DEAD box protein 5 (chains A)
GATNEVNVDAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTANVLYGKLKSE
GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG
QADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVE
KIVKKVLKD

Primary citation

Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1. Dossani, Z.Y., Weirich, C.S., Erzberger, J.P. et al. Proc Natl Acad Sci U S A (2009) 106:16251-16256. DOI 10.1073/pnas.0902251106 · 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
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

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