2DB3: ATP-dependent RNA helicase vasa

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Determined by X-ray diffraction at 2.2 Å resolution. Released 2 May 2006.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Drosophila melanogaster
Chains: 8
Atoms: 15,119
Mol. weight: 207.55 kDa
Ligands: MG, ANP
Released: 2 May 2006

Explore 2DB3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2DB3 contains 99 α-helices and 62 β-strands across 4 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: 25 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	204-208	5
α-helix	211-214	4
α-helix	225-230	6
β-strand	233-236	4	1
α-helix	240-244	5
α-helix	247-249	3
α-helix	254-262	9
α-helix	270-280	11
β-strand	285-288	4	1
α-helix	295-309	15
β-strand	321-324	4	1
α-helix	328-341	14
β-strand	351-352	2	1
α-helix	358-365	8
β-strand	371-374	4	1
α-helix	376-384	9
β-strand	395-399	5	1
α-helix	401-404	4
α-helix	410-418	9
β-strand	427-432	6	1
α-helix	437-444	8
β-strand	451-455	5	1
α-helix	460-462	3
β-strand	465-471	7	2
α-helix	474-476	3
α-helix	477-487	11
β-strand	492-495	4	2
α-helix	499-511	13
β-strand	516-519	4	2
α-helix	525-536	12
β-strand	542-545	4	2
α-helix	547-549	3
β-strand	560-563	4	2
α-helix	570-577	8
β-strand	587-593	7	2
α-helix	599-601	3
α-helix	602-611	10
α-helix	615-617	3
α-helix	618-620	3

Chain B: 24 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	204-208	5
α-helix	211-214	4
α-helix	225-230	6
β-strand	233-236	4	3
α-helix	240-244	5
α-helix	254-262	9
α-helix	270-280	11
β-strand	285-289	5	3
α-helix	295-309	15
β-strand	315	1	4
β-strand	318	1	4
β-strand	321-324	4	3
α-helix	328-341	14
β-strand	349-352	4	3
α-helix	358-366	9
β-strand	371-374	4	3
α-helix	376-384	9
β-strand	395-399	5	3
α-helix	401-404	4
α-helix	407-417	11
β-strand	427-432	6	3
α-helix	437-443	7
α-helix	444-446	3
β-strand	451-455	5	3
α-helix	460-462	3
β-strand	465-471	7	5
α-helix	474-476	3
α-helix	477-487	11
β-strand	492-495	4	5
α-helix	499-510	12
β-strand	516-519	4	5
α-helix	525-536	12
β-strand	542-545	4	5
α-helix	547-549	3
β-strand	560-563	4	5
α-helix	570-577	8
β-strand	587-593	7	5
α-helix	599-601	3
α-helix	602-611	10
α-helix	618-620	3

Chain C: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	204-208	5
α-helix	211-214	4
α-helix	225-230	6
β-strand	233-236	4	6
α-helix	240-244	5
α-helix	247-249	3
α-helix	254-262	9
α-helix	270-280	11
β-strand	285-288	4	6
α-helix	295-309	15
β-strand	315	1	7
β-strand	318	1	7
β-strand	321-324	4	6
α-helix	328-341	14
β-strand	349-352	4	6
α-helix	358-366	9
β-strand	371-374	4	6
α-helix	376-384	9
β-strand	395-398	4	6
α-helix	401-405	5
α-helix	407-417	11
β-strand	427-432	6	6
α-helix	437-443	7
α-helix	444-446	3
β-strand	451-455	5	6
α-helix	460-462	3
β-strand	465-471	7	8
α-helix	474-476	3
α-helix	477-487	11
β-strand	492-495	4	8
α-helix	499-511	13
β-strand	516-519	4	8
α-helix	525-536	12
β-strand	542-545	4	8
α-helix	547-549	3
β-strand	560-563	4	8
α-helix	570-577	8
β-strand	587-593	7	8
α-helix	599-601	3
α-helix	602-611	10
α-helix	618-620	3

Chain D: 25 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	204-208	5
α-helix	211-214	4
α-helix	226-230	5
β-strand	233-236	4	9
α-helix	240-244	5
α-helix	254-262	9
α-helix	270-280	11
β-strand	285-288	4	9
α-helix	295-309	15
β-strand	315	1	10
β-strand	318	1	10
β-strand	321-324	4	9
α-helix	328-341	14
α-helix	347-348	2
β-strand	349-352	4	9
α-helix	358-366	9
β-strand	371-374	4	9
α-helix	376-385	10
β-strand	395-399	5	9
α-helix	401-404	4
α-helix	407-417	11
β-strand	427-432	6	9
α-helix	437-443	7
α-helix	444-446	3
β-strand	451-455	5	9
α-helix	460-462	3
β-strand	465-471	7	11
α-helix	474-476	3
α-helix	477-487	11
β-strand	492-495	4	11
α-helix	499-510	12
β-strand	516-519	4	11
α-helix	525-536	12
β-strand	542-545	4	11
α-helix	547-549	3
β-strand	560-563	4	11
α-helix	570-577	8
β-strand	587-593	7	11
α-helix	599-611	13
α-helix	614-617	4
α-helix	618-620	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
5'-r(upupupupupupupupupu)-3'	E, F, G, H	RNA	10
ATP-dependent RNA helicase vasa	A, B, C, D	protein	434	Drosophila melanogaster	P09052 (AlphaFold model)

Sequence of entity 1 (E, F, G, H), FASTA

>2DB3_1 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' (chains E, F, G, H)
UUUUUUUUUU

Sequence of entity 2 (A, B, C, D), FASTA

>2DB3_2 ATP-dependent RNA helicase vasa (chains A, B, C, D)
GPLGSPEFPGEFYIPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTS
ADLRDIIIDNVNKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLE
DPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQNECITRGC
HVVIATPGRLLDFVDRTFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTL
MFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDVKQTIYEVNKYAKRSKLIEILSEQA
DGTIVFVETKRGADFLASFLSEKEFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSVA
SRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIAADLVKIL
EGSGQTVPDFLRTC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	4

Primary citation

Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Sengoku, T., Nureki, O., Nakamura, A. et al. Cell (2006) 125:287-300. DOI 10.1016/j.cell.2006.01.054 · PubMed

Other PDB entries of the same protein (UniProt P09052 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NT7 1.4 Å, Structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain…
3EMW 1.8 Å, Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 2…
3F2O 2.05 Å, Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 1…
2IHS 2.2 Å, Crystal structure of the B30.2/SPRY domain of GUSTAVUS in complex with a 20-residue VASA…

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