[English] 日本語
Yorodumi
- EMDB-75411: Human RNase PNK bound to ATPyS ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75411
TitleHuman RNase PNK bound to ATPyS ligand
Map dataComposite map of full molecule local refined EM maps
Sample
  • Complex: Human RNase PNK bound to ATPyS ligand
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsRibonuclease / Kinase / HEPN / LAS1L / NOL9 / ITS2 / Rixosome / RNA BINDING PROTEIN
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
Polynucleotide 5'-hydroxyl-kinase NOL9 / Ribosomal biogenesis protein LAS1L
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGordon J / Stanley RE
Funding support United States, 1 items
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 3, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75411.png

Downloads & links

-
Map

FileDownload / File: emd_75411.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of full molecule local refined EM maps
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.9
Minimum - Maximum-42.271369999999997 - 65.63355
Average (Standard dev.)0.0020179986 (±1.071578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Human RNase PNK bound to ATPyS ligand

EntireName: Human RNase PNK bound to ATPyS ligand
Components
  • Complex: Human RNase PNK bound to ATPyS ligand
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Human RNase PNK bound to ATPyS ligand

SupramoleculeName: Human RNase PNK bound to ATPyS ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Ribosomal biogenesis protein LAS1L

MacromoleculeName: Ribosomal biogenesis protein LAS1L / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.745586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMSWESGA GPGLGSQGMD LVWSAWYGKC VKGKGSLPLS AHGIVVAWL SRAEWDQVTV YLFCDDHKLQ RYALNRITVW RSRSGNELPL AVASTADLIR CKLLDVTGGL GTDELRLLYG M ALVRFVNL ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTMSWESGA GPGLGSQGMD LVWSAWYGKC VKGKGSLPLS AHGIVVAWL SRAEWDQVTV YLFCDDHKLQ RYALNRITVW RSRSGNELPL AVASTADLIR CKLLDVTGGL GTDELRLLYG M ALVRFVNL ISERKTKFAK VPLKCLAQEV NIPDWIVDLR HELTHKKMPH INDCRRGCYF VLDWLQKTYW CRQLENSLRE TW ELEEFRE GIEEEDQEED KNIVVDDITE QKPEPQDDGK STESDVKADG DSKGSEEVDS HCKKALSHKE LYERARELLV SYE EEQFTV LEKFRYLPKA IKAWNNPSPR VECVLAELKG VTCENREAVL DAFLDDGFLV PTFEQLAALQ IEYEDGQTEV QRGE GTDPK SHKNVDLNDV LVPKPFSQFW QPLLRGLHSQ NFTQALLERM LSELPALGIS GIRPTYILRW TVELIVANTK TGRNA RRFS AGQWEARRGW RLFNCSASLD WPRMVESCLG SPCWASPQLL RIIFKAMGQG LPDEEQEKLL RICSIYTQSG ENSLVQ EGS EASPIGKSPY TLDSLYWSVK PASSSFGSEA KAQQQEEQGS VNDVKEEEKE EKEVLPDQVE EEEENDDQEE EEEDEDD ED DEEEDRMEVG PFSTGQESPT AENARLLAQK RGALQGSAWQ VSSEDVRWDT FPLGRMPGQT EDPAELMLEN YDTMYLLD Q PVLEQRLEPS TCKTDTLGLS CGVGSGNCSN SSSSNFEGLL WSQGQLHGLK TGLQLF

UniProtKB: Ribosomal biogenesis protein LAS1L

-
Macromolecule #2: Polynucleotide 5'-hydroxyl-kinase NOL9

MacromoleculeName: Polynucleotide 5'-hydroxyl-kinase NOL9 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: polynucleotide 5'-hydroxyl-kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.119602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGGGGTASSC HRPLLIPPVR PVGPGRALLL LPVEQGFTFS GICRVTCLYG QVQVFGFTIS QGQPAQDIFS VYTHSCLSIH ALHYSQPEK SKKELKREAR NLLKSHLNLD DRRWSMQNFS PQCSIVLLEH LKTATVNFIT SYPGSSYIFV QESPTPQIKP E YLALRSVG ...String:
GGGGGTASSC HRPLLIPPVR PVGPGRALLL LPVEQGFTFS GICRVTCLYG QVQVFGFTIS QGQPAQDIFS VYTHSCLSIH ALHYSQPEK SKKELKREAR NLLKSHLNLD DRRWSMQNFS PQCSIVLLEH LKTATVNFIT SYPGSSYIFV QESPTPQIKP E YLALRSVG IRREKKRKGL QLTESTLSAL EELVNVSCEE VDGCPVILVC GSQDVGKSTF NRYLINHLLN SLPCVDYLEC DL GQTEFTP PGCISLLNIT EPVLGPPFTH LRTPQKMVYY GKPSCKNNYE NYIDIVKYVF SAYKRESPLI VNTMGWVSDQ GLL LLIDLI RLLSPSHVVQ FRSDHSKYMP DLTPQYVDDM DGLYTKSKTK MRNRRFRLAA FADALEFADE EKESPVEFTG HKLI GVYTD FAFRITPRNR ESHNKILRDL SILSYLSQLQ PPMPKPLSPL HSLTPYQVPF NAVALRITHS DVAPTHILYA VNASW VGLC KIQDDVRGYT NGPILLAQTP ICDCLGFGIC RGIDMEKRLY HILTPVPPEE LRTVNCLLVG AIAIPHCVLK CQRGIE GTV PYVTTDYNFK LPGASEKIGA REPEEAHKEK PYRRPKFCRK MK

UniProtKB: Polynucleotide 5'-hydroxyl-kinase NOL9

-
Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-10rn:
Human RNase PNK bound to ATPyS ligand

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more