4NHO: Spliceosomal DEAD-box protein Prp28

Structure of the spliceosomal DEAD-box protein Prp28. Determined by X-ray diffraction at 2.0 Å resolution. Released 18 Jun 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,833
Mol. weight: 56.1 kDa
Ligands: CXS, HG
Released: 18 Jun 2014

Explore 4NHO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NHO contains 33 α-helices and 15 β-strands across 1 chain. 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: 33 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	357-359	3
α-helix	362-364	3
α-helix	367-377	11
β-strand	379-382	4	1
α-helix	386-390	5
α-helix	400-409	10
α-helix	416-425	10
β-strand	431-434	4	1
α-helix	441-455	15
α-helix	458-461	4
β-strand	471-474	4	1
α-helix	478-492	15
α-helix	493-495	3
β-strand	499-502	4	1
α-helix	508-516	9
β-strand	521-524	4	1
α-helix	526-534	9
β-strand	545-548	4	1
α-helix	551-556	6
α-helix	560-567	8
α-helix	572-574	3
α-helix	576-577	2
α-helix	580-583	4
α-helix	585-593	9
α-helix	595-597	3
α-helix	598-600	3
β-strand	601-606	6	1
α-helix	611-620	10
α-helix	624	1
β-strand	625-629	5	1
α-helix	635-638	4
β-strand	640-645	6	2
α-helix	648-650	3
α-helix	651-660	10
β-strand	667-670	4	2
α-helix	674-686	13
β-strand	691-693	3	2
α-helix	704-712	9
β-strand	717-720	4	2
β-strand	735-738	4	2
α-helix	745-752	8
α-helix	753-755	3
β-strand	759-760	2	1
β-strand	763-768	6	2
α-helix	770-775	6
α-helix	776-784	9
α-helix	793-796	4
α-helix	799-801	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX23	A	protein	488	Homo sapiens	Q9BUQ8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NHO_1 Probable ATP-dependent RNA helicase DDX23 (chains A)
GPLGSARLRKLRKKEAKQRWDDRHWSQKKLDEMTDRDWRIFREDYSITTKGGKIPNPIRS
WKDSSLPPHILEVIDKCGYKEPTPIQRQAIPIGLQNRDIIGVAETGSGKTAAFLIPLLVW
ITTLPKIDRIEESDQGPYAIILAPTRELAQQIEEETIKFGKPLGIRTVAVIGGISREDQG
FRLRMGCEIVIATPGRLIDVLENRYLVLSRCTYVVLDEADRMIDMGFEPDVQKILEHMPV
SNQKPDTDEAEDPEKMLANFESGKHKYRQTVMFTATMPPAVERLARSYLRRPAVVYIGSA
GKPHERVEQKVFLMSESEKRKKLLAILEQGFDPPIIIFVNQKKGCDVLAKSLEKMGYNAC
TLHGGKGQEQREFALSNLKAGAKDILVATDVAGRGIDIQDVSMVVNYDMAKNIEDYIHRI
GRTGRAGKSGVAITFLTKEDSAVFYELKQAILESPVSSCPPELANHPDAQHKPGTILTKK
RREETIFA

Ligands and cofactors

ID	Name	Formula	Copies
CXS	3-cyclohexyl-1-propylsulfonic acid	C9 H19 N O3 S	1
HG	Mercury (II) ion	Hg	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28. Mohlmann, S., Mathew, R., Neumann, P. et al. Acta Crystallogr D Biol Crystallogr (2014) 70:1622-1630. DOI 10.1107/S1399004714006439 · PubMed

Other PDB entries of the same protein (UniProt Q9BUQ8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QW6 2.92 Å, Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution.
8Q91 3.1 Å, Structure of the human 20S U5 snRNP core
8QOZ 3.1 Å, Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part)
8H6E 3.2 Å, Cryo-EM structure of human exon-defined spliceosome in the late pre-B state.
8RC0 3.2 Å, Structure of the human 20S U5 snRNP
8H6J 3.25 Å, Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state.
6QX9 3.28 Å, Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
8Y6O 3.38 Å, Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11…
8QP8 3.5 Å, Cryo-EM Structure of Pre-B Complex (core part)
8QPA 3.7 Å, Cryo-EM Structure of Pre-B+5'ssLNG Complex (core part)
8QPB 3.7 Å, Cryo-EM Structure of Pre-B+ATP Complex (core part)
8Q7W 3.9 Å, Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 3)

Browse structure collections

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