3PEV: S. cerevisiae Dbp5 L327V C-terminal domain

S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 Mar 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,946
Mol. weight: 56.87 kDa
Ligands: IHP
Released: 23 Mar 2011

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

Secondary structure: helices and β-sheets

3PEV contains 33 α-helices and 13 β-strands across 2 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	305-310	6	1
α-helix	317-324	8
β-strand	332-336	5	1
α-helix	340-352	13
β-strand	357-360	4	1
α-helix	366-377	12
β-strand	383-386	4	1
β-strand	399-404	6	1
β-strand	409	1	2
β-strand	415	1	2
α-helix	417-424	8
α-helix	425-427	3
β-strand	435-440	6	1
α-helix	443-455	13
β-strand	462-465	4	1
α-helix	469-481	13

Chain B: 26 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	245-263	19
α-helix	264-268	5
α-helix	269-273	5
α-helix	276-289	14
α-helix	292-295	4
β-strand	299	1	3
α-helix	300-315	16
α-helix	321-338	18
α-helix	339-343	5
α-helix	344-345	2
α-helix	347-349	3
α-helix	350-363	14
α-helix	367-378	12
α-helix	380-383	4
α-helix	392-397	6
β-strand	402	1	4
β-strand	408	1	4
α-helix	409-410	2
α-helix	411-430	20
α-helix	432-434	3
α-helix	448-458	11
α-helix	462-464	3
α-helix	467-488	22
α-helix	490-497	8
α-helix	498-503	6
α-helix	504-506	3
α-helix	508-510	3
α-helix	513-526	14
α-helix	533-536	4
β-strand	537	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase DBP5	A	protein	188	Saccharomyces cerevisiae	P20449 (AlphaFold model)
Nucleoporin GLE1	B	protein	297	Saccharomyces cerevisiae	Q12315 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3PEV_1 ATP-dependent RNA helicase DBP5 (chains A)
GANEVNVDAIKQLYMDCKNEADKFDVLTELYGVMTIGSSIIFVATKKTANVLYGKLKSEG
HEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQ
ADPATYIHRIGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEK
IVKKVLKD

Sequence of entity 2 (B), FASTA

>3PEV_2 Nucleoporin GLE1 (chains B)
GATNFDKISKMFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQ
QLFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVHQAETEVRVKPESALPLGKLTLYLL
VQFPELQELFMARLVKKCPFVIGFTCEIDTEKGRQNMGWKRNNENKWEDNTSYDERMGGI
LSLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAA
VQFLQAYGNQASKLLILIGEELTSRMAEKKYVGAARLRILLEAWQNNNMESFPEMSP

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Water and common crystallization additives (GOL, SO4) 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
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
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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