3RRM: S. cerevisiae dbp5 l327v

S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp. Determined by X-ray diffraction at 2.9 Å resolution. Released 18 May 2011.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 8,323
Mol. weight: 122.6 kDa
Ligands: ADP, IHP, MG
Released: 18 May 2011

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

Secondary structure: helices and β-sheets

3RRM contains 48 α-helices and 59 β-strands across 3 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: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	101-109	9
α-helix	117-127	11
α-helix	131	1
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	235-238	4	1
α-helix	241-246	6
α-helix	250-260	11
β-strand	266-270	5	1
α-helix	276-285	10
β-strand	290-293	4	1
α-helix	301-303	3
β-strand	304-310	7	3
α-helix	316-324	9
β-strand	333-336	4	3
α-helix	340-353	14
β-strand	357-360	4	3
α-helix	366-377	12
β-strand	383-386	4	3
β-strand	399	1	4
β-strand	401-404	4	3
β-strand	409	1	5
β-strand	415	1	5
α-helix	417-425	9
β-strand	427	1	4
β-strand	434-440	7	3
α-helix	443-456	14
β-strand	461-465	5	3
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	290-294	5
β-strand	299	1	6
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	366-378	13
α-helix	380-383	4
α-helix	392-397	6
β-strand	402	1	7
β-strand	408	1	7
α-helix	409-410	2
α-helix	411-430	20
α-helix	432-434	3
α-helix	435-438	4
α-helix	448-459	12
α-helix	467-488	22
α-helix	490-497	8
α-helix	498-502	5
α-helix	503-506	4
α-helix	508-510	3
α-helix	513-526	14
α-helix	533-536	4
β-strand	537	1	6

Chain C: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	8
α-helix	7-9	3
β-strand	10-13	4	9
β-strand	17-25	9	10
β-strand	40	1	11
β-strand	42-45	4	12
β-strand	50-55	6	12
β-strand	58-63	6	12
α-helix	64-72	9
β-strand	82-85	4	12
β-strand	91-95	5	11
β-strand	98-102	5	11
β-strand	106-111	6	11
β-strand	118-123	6	11
β-strand	128-134	7	13
β-strand	137-142	6	13
β-strand	147-151	5	13
β-strand	157-161	5	13
β-strand	164-169	6	14
β-strand	173-178	6	14
β-strand	183-189	7	14
β-strand	192-199	8	14
α-helix	203-206	4
β-strand	214-220	7	8
β-strand	225-231	7	8
β-strand	245-253	9	8
β-strand	256-262	7	8
β-strand	278-284	7	9
β-strand	292-298	7	9
β-strand	303	1	15
β-strand	305-307	3	9
β-strand	312-315	4	9
α-helix	318-320	3
β-strand	323	1	15
α-helix	324-325	2
β-strand	326	1	16
β-strand	333	1	16
β-strand	338-342	5	10
α-helix	362-363	2
β-strand	364-368	5	10
β-strand	373-380	8	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase DBP5	A	protein	395	Saccharomyces cerevisiae	P20449 (AlphaFold model)
Nucleoporin GLE1	B	protein	297	Saccharomyces cerevisiae	Q12315 (AlphaFold model)
Nucleoporin NUP159	C	protein	388	Saccharomyces cerevisiae	P40477 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3RRM_1 ATP-dependent RNA helicase DBP5 (chains A)
GAMAKSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAA
FSLTMLTRVNPEDASPQAICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQI
NAQVIVGTPGTVLDLMRRKLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQL
VLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDAIKQLYMDCKNEADKFDVLTELYGV
MTIGSSIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITT
NVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKNSFN
ILSAIQKYFGDIEMTRVPTDDWDEVEKIVKKVLKD

Sequence of entity 2 (B), FASTA

>3RRM_2 Nucleoporin GLE1 (chains B)
GATNFDKISKMFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQ
QLFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVRQAETEVRVKPESALPLGKLTLYLL
VQFPELQELFMARLVKKCPFVIGFTCEIDTEKGRQNMGWKRNNENKWEDNTSYDERMGGI
LSLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAA
VQFLQAYGNQASKLLILIGEELTSRMAEKKYVGAARLRILLEAWQNNNMESFPEMSP

Sequence of entity 3 (C), FASTA

>3RRM_3 Nucleoporin NUP159 (chains C)
GASSLKDEVPTETSEDFGFKFLGQKQILPSFNEKLPFASLQNLDISNSKSLFVAASGSKA
VVGELQLLRDHITSDSTPLTFKWEKEIPDVIFVCFHGDQVLVSTRNALYSLDLEELSEFR
TVTSFEKPVFQLKNVNNTLVILNSVNDLSALDLRTKSTKQLAQNVTSFDVTNSQLAVLLK
DRSFQSFAWRNGEMEKQFEFSLPSELEELPVEEYSPLSVTILSPQDFLAVFGNVISETDD
EVSYDQKMYIIKHIDGSASFQETFDITPPFGQIVRFPYMYKVTLSGLIEPDANVNVLASS
CSSEVSIWDSKQVIEPSQDSERAVLPISEETDKDTNPIGVAVDVVTSGTILEPCSGVDTI
ERLPLVYILNNEGSLQIVGLFHVAAIKS

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1
MG	Magnesium ion	Mg	1

Primary citation

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 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
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
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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