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- EMDB-15606: CryoEM structure of the human Nucleophosmin 1 core -

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Basic information

Entry
Database: EMDB / ID: EMD-15606
TitleCryoEM structure of the human Nucleophosmin 1 core
Map data
Sample
  • Complex: Nucleophosmin 1
    • Protein or peptide: Nucleophosmin
Function / homology
Function and homology information


regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation ...regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation / SARS-CoV-1-host interactions / Tat protein binding / regulation of centrosome duplication / ALK mutants bind TKIs / spindle pole centrosome / Nuclear import of Rev protein / centrosome cycle / nucleocytoplasmic transport / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / protein kinase inhibitor activity / ribosomal large subunit binding / ribosomal small subunit binding / NF-kappaB binding / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / Nuclear events stimulated by ALK signaling in cancer / ribosomal subunit export from nucleus / core promoter sequence-specific DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / ribosome assembly / SUMOylation of transcription cofactors / ribosomal large subunit biogenesis / positive regulation of translation / protein-DNA complex / intracellular protein transport / PKR-mediated signaling / protein localization / : / cellular response to UV / cellular senescence / Signaling by ALK fusions and activated point mutants / unfolded protein binding / nucleosome assembly / ribosomal small subunit biogenesis / positive regulation of NF-kappaB transcription factor activity / histone binding / DNA-binding transcription factor binding / transcription coactivator activity / rRNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / DNA repair / focal adhesion / centrosome / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsValentin Gese G / Hallberg BM
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2017.0080 Sweden
CitationJournal: PNAS Nexus / Year: 2023
Title: A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1.
Authors: Mihkel Saluri / Axel Leppert / Genis Valentin Gese / Cagla Sahin / Dilraj Lama / Margit Kaldmäe / Gefei Chen / Arne Elofsson / Timothy M Allison / Marie Arsenian-Henriksson / Jan Johansson ...Authors: Mihkel Saluri / Axel Leppert / Genis Valentin Gese / Cagla Sahin / Dilraj Lama / Margit Kaldmäe / Gefei Chen / Arne Elofsson / Timothy M Allison / Marie Arsenian-Henriksson / Jan Johansson / David P Lane / B Martin Hällberg / Michael Landreh /
Abstract: How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant ...How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers and undergoes liquid-liquid phase separation by binding RNA or ribosomal proteins. It provides the scaffold for ribosome assembly but also prevents protein aggregation as part of the cellular stress response. Here, we use aggregation assays and native mass spectrometry (MS) to examine the relationship between the self-assembly and chaperone activity of NPM1. We find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning-based structure prediction and cryo-electron microscopy reveal fuzzy interactions between the acidic disordered region and the C-terminal nucleotide-binding domain, which cross-link NPM1 pentamers into partially disordered oligomers. The addition of basic peptides results in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. Together, our findings show that NPM1 uses a "grappling hook" mechanism to form a network-like structure that traps aggregation-prone proteins. Nucleolar proteins and RNAs simultaneously modulate the association strength and chaperone activity, suggesting a mechanism by which nucleolar composition regulates the chaperone activity of NPM1.
History
DepositionAug 18, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15606.png

Downloads & links

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Map

FileDownload / File: emd_15606.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.505 Å
Density
Contour LevelBy AUTHOR: 0.0015
Minimum - Maximum-0.0033958023 - 0.0079294825
Average (Standard dev.)1.1540068e-05 (±0.00016223617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 193.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15606_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_15606_additional_1.map
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Additional map: Nucleophosmin 1 class with weaker C-terminal domain density

Fileemd_15606_additional_2.map
AnnotationNucleophosmin 1 class with weaker C-terminal domain density
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Additional map: Nucleophosmin 1 class with stronger C-terminal domain density

Fileemd_15606_additional_3.map
AnnotationNucleophosmin 1 class with stronger C-terminal domain density
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Half map: #2

Fileemd_15606_half_map_1.map
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Half map: #1

Fileemd_15606_half_map_2.map
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Sample components

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Entire : Nucleophosmin 1

EntireName: Nucleophosmin 1
Components
  • Complex: Nucleophosmin 1
    • Protein or peptide: Nucleophosmin

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Supramolecule #1: Nucleophosmin 1

SupramoleculeName: Nucleophosmin 1 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nucleophosmin

MacromoleculeName: Nucleophosmin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.708141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMEDSMDMDM SPLRPQNYLF GCELKADKDY HFKVDNDENE HQLSLRTVSL GAGAKDELHI VEAEAMNYEG SPIKVTLATL KMSVQPTVS LGGFEITPPV VLRLKCGSGP VHISGQHLVA VEEDAESEDE EEEDVKLLSI SGKRSAPGGG SKVPQKKVKL A ADEDDDDD ...String:
SMEDSMDMDM SPLRPQNYLF GCELKADKDY HFKVDNDENE HQLSLRTVSL GAGAKDELHI VEAEAMNYEG SPIKVTLATL KMSVQPTVS LGGFEITPPV VLRLKCGSGP VHISGQHLVA VEEDAESEDE EEEDVKLLSI SGKRSAPGGG SKVPQKKVKL A ADEDDDDD DEEDDDEDDD DDDFDDEEAE EKAPVKKSIR DTPAKNAQKS NQNGKDSKPS STPRSKGQES FKKQEKTPKT PK GPSSVED IKAKMQASIE KGGSLPKVEA KFINYVKNCF RMTDQEAIQD LWQWRKSL

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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

Concentration0.75 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106905
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ehd

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-8as5:
CryoEM structure of the human Nucleophosmin 1 core

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