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- PDB-10rr: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site -

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Basic information

Entry
Database: PDB / ID: 10rr
TitleHuman RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
Components
  • CAA RNA
  • Polynucleotide 5'-hydroxyl-kinase NOL9
  • Ribosomal biogenesis protein LAS1L
KeywordsRNA BINDING PROTEIN / Ribonuclease / Kinase / RNA / HEPN / LAS1L / NOL9 / ITS2 / Rixosome
Function / homology
Function and homology information


ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase / polynucleotide 5'-hydroxyl-kinase activity / rixosome complex / Las1 complex / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / maturation of 5.8S rRNA / MLL1 complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol ...ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase / polynucleotide 5'-hydroxyl-kinase activity / rixosome complex / Las1 complex / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / maturation of 5.8S rRNA / MLL1 complex / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA / rRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
: / : / Polynucleotide 5'-hydroxyl-kinase NOL9, N-terminal domain / NOL9-like, C-terminal domain / Las1 / Las1-like / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / Polynucleotide 5'-hydroxyl-kinase NOL9 / Ribosomal biogenesis protein LAS1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGordon, J. / Stanley, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural insights into RNA phosphorylation by the RNase PNK module of the human rixosome complex.
Authors: Jacob Gordon / Savannah M Seely / Huanchen Wang / Juno M Krahn / Wyatt A Peele / Mario J Borgnia / Alan J Warren / Robin E Stanley /
Abstract: The mammalian rixosome complex is a large multi-subunit complex that plays essential roles in ribosome assembly and heterochromatin maintenance. Three structural proteins form the stable core of the ...The mammalian rixosome complex is a large multi-subunit complex that plays essential roles in ribosome assembly and heterochromatin maintenance. Three structural proteins form the stable core of the rixosome to which three enzymatic modules are flexibly tethered including an RNA processing module, AAA-ATPase, and SUMO protease. The RNA processing module is formed by RNase PNK, a tetrameric assembly comprising two copies each of the LAS1L endoribonuclease (RNase) and the NOL9 polynucleotide kinase (PNK). Using single particle cryo-EM, we determined ATPγS and AMP-PNP/RNA-bound structures of human RNase PNK. The structures revealed the overall butterfly-like architecture of the complex and provide new insights into the mechanism of RNA accommodation and 5' hydroxyl phosphorylation within the NOL9 active site. Through reconstitution studies and molecular modeling, we establish how RNase PNK is incorporated into the larger rixosome complex by a distinct domain of LAS1L. Finally, we show that the human 5'-3' exoribonuclease XRN2 directly associates with RNase PNK and selectively degrades NOL9-phosphorylated RNA in vitro, thereby linking ITS2 processing by the rixosome to processive exonucleolytic decay. Collectively this work establishes an updated model for how the rixosome integrates its diverse enzymatic activities to regulate ITS2 processing.
History
DepositionFeb 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal biogenesis protein LAS1L
B: Polynucleotide 5'-hydroxyl-kinase NOL9
C: CAA RNA
D: Ribosomal biogenesis protein LAS1L
E: Polynucleotide 5'-hydroxyl-kinase NOL9
F: CAA RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,30410
Polymers313,2436
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ribosomal biogenesis protein LAS1L / Endoribonuclease LAS1L / Protein LAS1 homolog


Mass: 87583.367 Da / Num. of mol.: 2 / Mutation: R155E, H156A, H160A
Source method: isolated from a genetically manipulated source
Details: True M amnio acid position 1 of protein is located at position 84 in alignment due to N-terminal StrepII-FLAG tag present. Position 232 (L) in alignment is amino acid 625 in true protein. ...Details: True M amnio acid position 1 of protein is located at position 84 in alignment due to N-terminal StrepII-FLAG tag present. Position 232 (L) in alignment is amino acid 625 in true protein. True residues 189-624 of protein were not modeled and are omitted from alignment.
Source: (gene. exp.) Homo sapiens (human) / Gene: LAS1L, MSTP060 / Cell line (production host): HEK293Tf / Production host: Homo sapiens (human)
References: UniProt: Q9Y4W2, Hydrolases; Acting on ester bonds
#2: Protein Polynucleotide 5'-hydroxyl-kinase NOL9 / Nucleolar protein 9


Mass: 68119.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOL9 / Cell line (production host): HEK293Tf / Production host: Homo sapiens (human)
References: UniProt: Q5SY16, polynucleotide 5'-hydroxyl-kinase
#3: RNA chain CAA RNA


Mass: 918.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293Tf
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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