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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 / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / Las1 complex / polynucleotide 5'-hydroxyl-kinase activity / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MLL1 complex / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA ...ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity / polynucleotide 5'-hydroxyl-kinase / ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity / Las1 complex / polynucleotide 5'-hydroxyl-kinase activity / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / MLL1 complex / Major pathway of rRNA processing in the nucleolus and cytosol / maturation of LSU-rRNA / rRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / hydrolase activity / nucleolus / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
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: To Be Published
Title: Structural Insights into RNA Phosphorylation by the RNase PNK Module of the Human Rixosome Complex.
Authors: Gordon, J. / Stanley, R.E.
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

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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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