4JKD: Pre-mRNA-processing-splicing factor 8

Open and closed forms of I1790Y human PRP8 RNase H-like domain with bound Mg ion. Determined by X-ray diffraction at 1.55 Å resolution. Released 22 May 2013.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,385
Mol. weight: 51.37 kDa
Ligands: MG
Released: 22 May 2013

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

Secondary structure: helices and β-sheets

4JKD contains 25 α-helices and 14 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1777-1781	5	1
β-strand	1787-1792	6	2
β-strand	1798-1803	6	2
β-strand	1805-1810	6	1
β-strand	1816-1822	7	1
α-helix	1824-1827	4
α-helix	1833-1851	19
α-helix	1854-1856	3
β-strand	1860-1863	4	1
α-helix	1866-1868	3
α-helix	1869-1875	7
β-strand	1883-1886	4	1
α-helix	1893-1898	6
α-helix	1900-1908	9
β-strand	1913-1918	6	1
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1947-1953	7
α-helix	1973-1988	16

Chain B: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	1777-1784	8	3
α-helix	1788-1792	5
α-helix	1801-1803	3
β-strand	1805-1810	6	3
β-strand	1816-1822	7	3
α-helix	1827-1829	3
α-helix	1836-1837	2
α-helix	1838-1851	14
α-helix	1854-1856	3
β-strand	1860-1863	4	3
α-helix	1866-1868	3
α-helix	1869-1875	7
β-strand	1883-1886	4	3
α-helix	1893-1898	6
α-helix	1900-1908	9
β-strand	1913-1918	6	3
α-helix	1923-1925	3
α-helix	1929-1945	17
α-helix	1947-1953	7
α-helix	1973-1988	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-mRNA-processing-splicing factor 8	A, B	protein	222	Homo sapiens	Q6P2Q9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4JKD_1 Pre-mRNA-processing-splicing factor 8 (chains A, B)
GELFSNQIIWFVDDTNVYRVTYHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWA
GQKRLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPNIVIKGSE
LQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYTAFSRLILILRALHVNND
RAKVILKPDKTTITEPHHIWPTLTDEEWIKVEVQLKDLILAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

Primary citation

A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Schellenberg, M.J., Wu, T., Ritchie, D.B. et al. Nat Struct Mol Biol (2013) 20:728-734. DOI 10.1038/nsmb.2556 · PubMed

Other PDB entries of the same protein (UniProt Q6P2Q9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4JK8 1.15 Å, Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Mg ion
4JKB 1.3 Å, Open and closed forms of V1788D human PRP8 RNase H-like domain with bound Mg ion
4JKA 1.32 Å, Open and closed forms of R1865A human PRP8 RNase H-like domain with bound Co ion
4JK7 1.4 Å, Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Mg ion
4JK9 1.5 Å, Open and closed forms of wild-type human PRP8 RNase H-like domain with bound Co ion
4JKC 1.5 Å, Open and closed forms of T1800E human PRP8 RNase H-like domain with bound Mg ion
4JKE 1.65 Å, Open and closed forms of T1789P human PRP8 RNase H-like domain with bound Mg ion
4JKG 1.8 Å, Open and closed forms of mixed T1789P+R1865A and R1865A human PRP8 RNase H-like domain…
4JKH 1.8 Å, Open and closed forms of D1781E human PRP8 RNase H-like domain with bound Mg ion
3ENB 1.85 Å, Crystal Structure of PRP8 core domain IV
3LRU 1.85 Å, hPRP8 Non-Native Subdomain
3E9L 1.95 Å, Crystal Structure of Human Prp8, Residues 1755-2016

Browse structure collections

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