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- EMDB-75414: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75414
TitleHuman RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
Map dataComposite map
Sample
  • Complex: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
    • RNA: CAA RNA
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsRibonuclease / Kinase / RNA / 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 / 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
Polynucleotide 5'-hydroxyl-kinase NOL9 / Ribosomal biogenesis protein LAS1L
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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: To Be Published
Title: Structural Insights into RNA Phosphorylation by the RNase PNK Module of the Human Rixosome Complex.
Authors: Gordon J / Stanley RE
History
DepositionFeb 4, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75414.png

Downloads & links

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Map

FileDownload / File: emd_75414.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.66 Å/pix.
x 504 pix.
= 332.64 Å		0.66 Å/pix.
x 504 pix.
= 332.64 Å		0.66 Å/pix.
x 504 pix.
= 332.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.1
Minimum - Maximum-47.687714 - 63.892845000000001
Average (Standard dev.)-0.0031389536 (±1.0314157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 332.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site

EntireName: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
Components
  • Complex: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
    • Protein or peptide: Ribosomal biogenesis protein LAS1L
    • Protein or peptide: Polynucleotide 5'-hydroxyl-kinase NOL9
    • RNA: CAA RNA
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site

SupramoleculeName: Human RNase PNK bound to AMPPNP ligand + rCAA in PNK active site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ribosomal biogenesis protein LAS1L

MacromoleculeName: Ribosomal biogenesis protein LAS1L / type: protein_or_peptide / ID: 1
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.
Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.583367 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 NIPDWIVDLE AELTAKKMPH 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

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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

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Macromolecule #3: CAA RNA

MacromoleculeName: CAA RNA / type: rna / ID: 3 / Number of copies: 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 918.636 Da
SequenceString:
CAA

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Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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

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