10RR: Human RNase PNK

Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site. Determined by electron microscopy at 3.5 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,366
Mol. weight: 314.3 kDa
Ligands: MG, ANP
Released: 26 Aug 2026

Explore 10RR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

10RR contains 54 α-helices and 54 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.

Chains A and D: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	49-55	7
α-helix	66-78	13
α-helix	88-99	12
α-helix	108-125	18
α-helix	150-158	9
α-helix	169-183	15
α-helix	629-632	4
β-strand	639-640	2	1
α-helix	641-642	2
α-helix	647-649	3
β-strand	671-673	3	2

Chains B and E: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	114-116	3
β-strand	117-120	4	3
β-strand	123-127	5	3
β-strand	134-137	4	4
β-strand	138-146	9	3
β-strand	149-151	3	4
β-strand	154-156	3	4
α-helix	161-162	2
β-strand	163-167	5	3
β-strand	174-176	3	4
α-helix	188-198	11
α-helix	205-211	7
β-strand	221-226	6	3
α-helix	230-237	8
α-helix	242-244	3
α-helix	256-264	9
β-strand	267-268	2	4
α-helix	279-293	15
α-helix	312-324	13
β-strand	330-332	3	5
β-strand	347-348	2	6
β-strand	351-353	3	5
β-strand	372-373	2	6
α-helix	384-394	11
α-helix	414-425	12
β-strand	433	1	7
α-helix	447-451	5
β-strand	500	1	7
α-helix	512-528	17
α-helix	529-531	3
α-helix	538-539	2
α-helix	542-544	3
β-strand	548-549	2	1
β-strand	551	1	8
β-strand	556-557	2	2
β-strand	558-559	2	8
α-helix	566-571	6
β-strand	577-581	5	8
β-strand	595-597	3	2
β-strand	605-615	11	8
β-strand	620-624	5	8
α-helix	629-632	4
β-strand	639-640	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ribosomal biogenesis protein LAS1L	A, D	protein	777	Homo sapiens	Q9Y4W2 (AlphaFold model)
Polynucleotide 5'-hydroxyl-kinase NOL9	B, E	protein	605	Homo sapiens	Q5SY16 (AlphaFold model)
Caa RNA	C, F	RNA	3	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>10RR_1 Ribosomal biogenesis protein LAS1L (chains A, D)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMSWESGAGPGLGSQGMD
LVWSAWYGKCVKGKGSLPLSAHGIVVAWLSRAEWDQVTVYLFCDDHKLQRYALNRITVWR
SRSGNELPLAVASTADLIRCKLLDVTGGLGTDELRLLYGMALVRFVNLISERKTKFAKVP
LKCLAQEVNIPDWIVDLEAELTAKKMPHINDCRRGCYFVLDWLQKTYWCRQLENSLRETW
ELEEFREGIEEEDQEEDKNIVVDDITEQKPEPQDDGKSTESDVKADGDSKGSEEVDSHCK
KALSHKELYERARELLVSYEEEQFTVLEKFRYLPKAIKAWNNPSPRVECVLAELKGVTCE
NREAVLDAFLDDGFLVPTFEQLAALQIEYEDGQTEVQRGEGTDPKSHKNVDLNDVLVPKP
FSQFWQPLLRGLHSQNFTQALLERMLSELPALGISGIRPTYILRWTVELIVANTKTGRNA
RRFSAGQWEARRGWRLFNCSASLDWPRMVESCLGSPCWASPQLLRIIFKAMGQGLPDEEQ
EKLLRICSIYTQSGENSLVQEGSEASPIGKSPYTLDSLYWSVKPASSSFGSEAKAQQQEE
QGSVNDVKEEEKEEKEVLPDQVEEEEENDDQEEEEEDEDDEDDEEEDRMEVGPFSTGQES
PTAENARLLAQKRGALQGSAWQVSSEDVRWDTFPLGRMPGQTEDPAELMLENYDTMYLLD
QPVLEQRLEPSTCKTDTLGLSCGVGSGNCSNSSSSNFEGLLWSQGQLHGLKTGLQLF

Sequence of entity 2 (B, E), FASTA

>10RR_2 Polynucleotide 5'-hydroxyl-kinase NOL9 (chains B, E)
GGGGGTASSCHRPLLIPPVRPVGPGRALLLLPVEQGFTFSGICRVTCLYGQVQVFGFTIS
QGQPAQDIFSVYTHSCLSIHALHYSQPEKSKKELKREARNLLKSHLNLDDRRWSMQNFSP
QCSIVLLEHLKTATVNFITSYPGSSYIFVQESPTPQIKPEYLALRSVGIRREKKRKGLQL
TESTLSALEELVNVSCEEVDGCPVILVCGSQDVGKSTFNRYLINHLLNSLPCVDYLECDL
GQTEFTPPGCISLLNITEPVLGPPFTHLRTPQKMVYYGKPSCKNNYENYIDIVKYVFSAY
KRESPLIVNTMGWVSDQGLLLLIDLIRLLSPSHVVQFRSDHSKYMPDLTPQYVDDMDGLY
TKSKTKMRNRRFRLAAFADALEFADEEKESPVEFTGHKLIGVYTDFAFRITPRNRESHNK
ILRDLSILSYLSQLQPPMPKPLSPLHSLTPYQVPFNAVALRITHSDVAPTHILYAVNASW
VGLCKIQDDVRGYTNGPILLAQTPICDCLGFGICRGIDMEKRLYHILTPVPPEELRTVNC
LLVGAIAIPHCVLKCQRGIEGTVPYVTTDYNFKLPGASEKIGAREPEEAHKEKPYRRPKF
CRKMK

Sequence of entity 3 (C, F), FASTA

>10RR_3 CAA RNA (chains C, F)
CAA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Structural insights into RNA phosphorylation by the RNase PNK module of the human rixosome complex. Gordon, J., Seely, S.M., Wang, H. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag826 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4W2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8FL3 2.53 Å, Human nuclear pre-60S ribosomal subunit (State I2)
8FL2 2.67 Å, Human nuclear pre-60S ribosomal subunit (State I1)
8FL4 2.89 Å, Human nuclear pre-60S ribosomal subunit (State I3)
9DUN 3.32 Å, Human LAS1L-NOL9 complex
26LK 3.4 Å, Cryo-EM structure of human LAS1L-NOL9 complex
10RN 3.6 Å, Human RNase PNK bound to ATPyS ligand

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