6SH6: Human DEAH-helicase DHX15

Crystal structure of the human DEAH-helicase DHX15 in complex with the NKRF G-patch bound to ADP. Determined by X-ray diffraction at 1.85 Å resolution. Released 22 Apr 2020.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,159
Mol. weight: 87 kDa
Ligands: MG, ADP
Released: 22 Apr 2020

Explore 6SH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SH6 contains 46 α-helices and 30 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: 43 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	116	1	1
β-strand	121	1	1
α-helix	122-124	3
α-helix	125-134	10
α-helix	138-142	5
α-helix	143-150	8
β-strand	155-159	5	2
α-helix	166-179	14
β-strand	187-192	6	2
α-helix	195-208	14
β-strand	213	1	2
β-strand	217-221	5	2
β-strand	224-226	3	2
β-strand	233-237	5	2
α-helix	238-245	8
β-strand	254-259	6	2
α-helix	262-264	3
α-helix	267-282	16
β-strand	287-292	6	2
α-helix	296-298	3
α-helix	299-303	5
β-strand	309-311	3	2
α-helix	312-314	3
α-helix	316-318	3
β-strand	319-323	5	3
α-helix	331-345	15
β-strand	351-355	5	3
α-helix	359-374	16
α-helix	381-382	2
β-strand	383-388	6	3
α-helix	394-397	4
α-helix	398-401	4
α-helix	403-406	4
β-strand	415-420	6	3
α-helix	423-426	4
β-strand	433-438	6	3
β-strand	441-448	8	4
β-strand	453-460	8	4
α-helix	461-462	2
α-helix	463-471	9
α-helix	472-474	3
β-strand	479-483	5	3
α-helix	487-493	7
α-helix	498-500	3
α-helix	501-503	3
α-helix	508-516	9
α-helix	530-532	3
α-helix	533-545	13
β-strand	549	1	5
α-helix	554	1
β-strand	555	1	5
α-helix	556	1
α-helix	557-563	7
α-helix	569-578	10
α-helix	579-581	3
α-helix	584-594	11
β-strand	600	1	6
α-helix	607-615	9
β-strand	619	1	7
β-strand	622	1	7
α-helix	623-636	14
α-helix	641-646	6
β-strand	649	1	6
α-helix	651-670	20
α-helix	684-697	14
β-strand	701-704	4	7
β-strand	710-712	3	7
β-strand	718-721	4	7
β-strand	733-741	9	7
β-strand	745-752	8	7
α-helix	755-761	7
α-helix	771-772	2
α-helix	775-788	14

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	554-561	8
α-helix	582-586	5
α-helix	589-590	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15	A	protein	689	Homo sapiens	O43143 (AlphaFold model)
NF-kappa-B-repressing factor	B	protein	67	Homo sapiens	O15226 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SH6_1 Pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 (chains A)
GPHMLEQCINPFTNLPHTPRYYDILKKRLQLPVWEYKDRFTDILVRHQSFVLVGETGSGK
TTQIPQWCVEYMRSLPGPKRGVACTQPRRVAAMSVAQRVADEMDVMLGQEVGYSIRFEDC
SSAKTILKYMTDGMLLREAMNDPLLERYGVIILDEAHERTLATDILMGVLKEVVRQRSDL
KVIVMSATLDAGKFQIYFDNCPLLTIPGRTHPVEIFYTPEPERDYLEAAIRTVIQIHMCE
EEEGDLLLFLTGQEEIDEACKRIKREVDDLGPEVGDIKIIPLYSTLPPQQQQRIFEPPPP
KKQNGAIGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVTAISKASA
QQRAGRAGRTRPGKCFRLYTEKAYKTEMQDNTYPEILRSNLGSVVLQLKKLGIDDLVHFD
FMDPPAPETLMRALELLNYLAALNDDGDLTELGSMMAEFPLDPQLAKMVIASCDYNCSNE
VLSITAMLSVPQCFVRPTEAKKAADEAKMRFAHIDGDHLTLLNVYHAFKQNHESVQWCYD
NFINYRSLMSADNVRQQLSRIMDRFNLPRRSTDFTSRDYYINIRKALVTGYFMQVAHLER
TGHYLTVKDNQVVQLHPSTVLDHKPEWVLYNEFVLTTKNYIRTCTDIKPEWLVKIAPQYY
DMSNFPQCEAKRQLDRIIAKLQSKEYSQY

Sequence of entity 2 (B), FASTA

>6SH6_2 NF-kappa-B-repressing factor (chains B)
GPHMAEEAYKQQIKEDNIGNQLLRKMGWTGGGLGKSGEGIREPISVKEQHKREGLGLDVE
RVNKIAK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural basis for DEAH-helicase activation by G-patch proteins. Studer, M.K., Ivanovic, L., Weber, M.E. et al. Proc Natl Acad Sci U S A (2020) 117:7159-7170. DOI 10.1073/pnas.1913880117 · PubMed

Other PDB entries of the same protein (UniProt O43143 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EJM 1.8 Å, Crystal structure of human DEAH-box helicase DHX15 in complex with SUGP1 G-patch
5XDR 2.0 Å, Crystal structure of human DEAH-box RNA helicase DHX15 in complex with ADP
6SH7 2.21 Å, Crystal structure of the human DEAH-helicase DHX15 in complex with the NKRF G-patch
9S2E 2.4 Å, Human intron-lariat spliceosome-Aquarius (ILSaqr)
6ID1 2.86 Å, Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex)…
9ZE0 3.43 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15…
8RO2 3.5 Å, Integrative Structure of the human intron lariat Spliceosome (ILS'')
9ZE3 3.93 Å, Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15…
9R8V 8.5 Å, Cryo-EM structure of the human pre-Bact-OTS complex (whole map)

Browse structure collections

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