5SUP: Sub2-Yra1 complex in association with RNA

Crystal structure of the Sub2-Yra1 complex in association with RNA. Determined by X-ray diffraction at 2.6 Å resolution. Released 18 Jan 2017.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Saccharomyces cerevisiae, SYNTHETIC CONSTRUCT
Chains: 9
Atoms: 10,127
Mol. weight: 159.62 kDa
Ligands: MG, BEF, ADP
Released: 18 Jan 2017

Explore 5SUP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5SUP contains 64 α-helices and 42 β-strands across 6 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: 21 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	63-67	5
α-helix	71-79	9
α-helix	87-96	10
β-strand	102-105	4	1
α-helix	113-123	11
β-strand	133-136	4	1
α-helix	140-153	14
β-strand	162-165	4	1
α-helix	171-179	9
β-strand	187-190	4	1
α-helix	192-199	8
β-strand	211-215	5	1
α-helix	217-222	6
α-helix	224-234	11
β-strand	242-247	6	1
α-helix	255-259	5
β-strand	266-268	3	1
α-helix	273-276	4
β-strand	281-287	7	2
α-helix	290-292	3
α-helix	293-303	11
β-strand	308-312	5	2
α-helix	316-328	13
β-strand	333-336	4	2
α-helix	342-353	12
β-strand	359-362	4	2
α-helix	364-366	3
β-strand	375-380	6	2
α-helix	387-394	8
α-helix	399-401	3
β-strand	404-410	7	2
α-helix	413-426	14
β-strand	431-432	2	2
α-helix	433-434	2
α-helix	441-443	3

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	64-67	4
α-helix	71-79	9
α-helix	87-97	11
β-strand	102-105	4	3
α-helix	113-123	11
β-strand	133-136	4	3
α-helix	140-153	14
β-strand	162-165	4	3
α-helix	171-179	9
β-strand	187-190	4	3
α-helix	192-200	9
β-strand	211-215	5	3
α-helix	217-222	6
α-helix	224-234	11
β-strand	242-247	6	3
α-helix	255-259	5
β-strand	266-268	3	3
α-helix	273-276	4
β-strand	281-287	7	4
α-helix	290-292	3
α-helix	293-303	11
β-strand	308-312	5	4
α-helix	316-328	13
β-strand	333-336	4	4
α-helix	342-353	12
β-strand	359-362	4	4
α-helix	364-366	3
β-strand	375-380	6	4
α-helix	387-394	8
β-strand	404-410	7	4
α-helix	413-425	13
β-strand	431-432	2	4
α-helix	433-434	2
α-helix	440-443	4

Chain C: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	65-67	3
α-helix	71-79	9
α-helix	87-96	10
β-strand	102-105	4	5
α-helix	113-123	11
β-strand	133-136	4	5
α-helix	140-153	14
β-strand	162-165	4	5
α-helix	171-179	9
β-strand	187-190	4	5
α-helix	192-199	8
β-strand	211-215	5	5
α-helix	217-222	6
α-helix	224-234	11
β-strand	242-247	6	5
α-helix	255-259	5
β-strand	266-268	3	5
α-helix	273-276	4
β-strand	281-287	7	6
α-helix	290-292	3
α-helix	293-303	11
β-strand	308-312	5	6
α-helix	316-328	13
β-strand	333-336	4	6
α-helix	342-353	12
β-strand	359-362	4	6
α-helix	364-366	3
β-strand	375-380	6	6
α-helix	387-394	8
β-strand	404-410	7	6
α-helix	413-426	14
β-strand	431-432	2	6
α-helix	433-434	2
α-helix	440-443	4

Chains G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	212-222	11

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	212-223	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ATP-dependent RNA helicase SUB2	A, B, C	protein	390	Saccharomyces cerevisiae	Q07478 (AlphaFold model)
RNA annealing protein YRA1	G, H, I	protein	32	Saccharomyces cerevisiae	Q12159 (AlphaFold model)
RNA (5'-r(pupupupupupu)-3')	D, E, F	RNA	15	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, B, C), FASTA

>5SUP_1 ATP-dependent RNA helicase SUB2 (chains A, B, C)
GAMGSTGFKDFLLKPELSRAIIDCGFEHPSEVQQHTIPQSIHGTDVLCQAKSGLGKTAVF
VLSTLQQLDPVPGEVAVVVICNARELAYQIRNEYLRFSKYMPDVKTAVFYGGTPISKDAE
LLKNKDTAPHIVVATPGRLKALVREKYIDLSHVKNFVIDECDKVLEELDMRRDVQEIFRA
TPRDKQVMMFSATLSQEIRPICRRFLQNPLEIFVDDEAKLTLHGLQQYYIKLEEREKNRK
LAQLLDDLEFNQVIIFVKSTTRANELTKLLNASNFPAITVHGHMKQEERIARYKAFKDFE
KRICVSTDVFGRGIDIERINLAINYDLTNEADQYLHRVGRAGRFGTKGLAISFVSSKEDE
EVLAKIQERFDVKIAEFPEEGIDPSTYLNN

Sequence of entity 2 (G, H, I), FASTA

>5SUP_2 RNA annealing protein YRA1 (chains G, H, I)
GAMGSNKPKREKPAKKSLEDLDKEMADYFEKK

Sequence of entity 3 (D, E, F), FASTA

>5SUP_3 RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') (chains D, E, F)
UUUUUUUUUUUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
BEF	Beryllium trifluoride ion	Be F3	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1. Ren, Y., Schmiege, P., Blobel, G. Elife (2017) 6. DOI 10.7554/eLife.20070 · PubMed

Other PDB entries of the same protein (UniProt Q07478 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8U8C 2.4 Å, Crystal structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
8U8D 3.04 Å, Cryo-EM structure of the TREX-2 complex in complex with the N-terminal motif of Sub2
8U8E 3.33 Å, Cryo-EM structure of the TREX-2 complex in association with Sub2
7APX 3.4 Å, yeast THO-Sub2 complex
7V2Y 3.4 Å, cryo-EM structure of yeast THO complex with Sub2
7LUV 3.7 Å, Cryo-EM structure of the yeast THO-Sub2 complex
9ZEB 3.72 Å, Cryo-EM structure of the TREX-2.1 complex (Thp3/Csn12/Sem1) bound to the DEAD-box ATPase…
7AQO 4.5 Å, yeast THO-Sub2 complex dimer
5SUQ 6.0 Å, Crystal structure of the THO-Sub2 complex

Browse structure collections

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