[English] 日本語
Yorodumi
- PDB-8as5: CryoEM structure of the human Nucleophosmin 1 core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8as5
TitleCryoEM structure of the human Nucleophosmin 1 core
ComponentsNucleophosmin
KeywordsCHAPERONE / Phase separation
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 / unfolded protein binding / Signaling by ALK fusions and activated point mutants / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsValentin Gese, G. / Hallberg, B.M.
Funding support Sweden, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleophosmin
B: Nucleophosmin
C: Nucleophosmin
D: Nucleophosmin
E: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)163,5415
Polymers163,5415
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A
137A
147A
158A
168A
179A
189A
1910A
2010A

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A15 - 117
211A15 - 117
322A15 - 117
422A15 - 117
533A15 - 116
633A15 - 116
744A15 - 117
844A15 - 117
955A14 - 118
1055A14 - 118
1166A14 - 118
1266A14 - 118
1377A14 - 118
1477A14 - 118
1588A14 - 118
1688A14 - 118
1799A14 - 119
1899A14 - 119
191010A14 - 118
201010A14 - 118

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20

-
Components

#1: Protein
Nucleophosmin / NPM / Nucleolar phosphoprotein B23 / Nucleolar protein NO38 / Numatrin


Mass: 32708.141 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPM1, NPM / Production host: Escherichia coli (E. coli) / References: UniProt: P06748

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Nucleophosmin 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: REFMAC / Version: 5.8.0352 / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
7Coot0.9.8.1model fitting
9cryoSPARCinitial Euler assignment
10RELIONfinal Euler assignment
19REFMAC5.8.0352model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106905 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model buildingPDB-ID: 5EHD

5ehd

RefinementResolution: 2.5→91.91 Å / Cor.coef. Fo:Fc: 0.918 / WRfactor Rwork: 0.53 / SU B: 26.486 / SU ML: 0.458 / Average fsc free: 0 / Average fsc overall: 0.3441 / Average fsc work: 0.3441 / Cross valid method: NONE / ESU R: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.53 89499 -
all0.53 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 126.735 Å2
Refinement stepCycle: 1 / Total: 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.0123741
ELECTRON MICROSCOPYr_bond_other_d00.0163574
ELECTRON MICROSCOPYr_angle_refined_deg1.0451.6525052
ELECTRON MICROSCOPYr_angle_other_deg0.321.5718341
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.7215465
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.781510
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.50410645
ELECTRON MICROSCOPYr_dihedral_angle_6_deg14.09910142
ELECTRON MICROSCOPYr_chiral_restr0.0460.2597
ELECTRON MICROSCOPYr_chiral_restr_other0.0260.25
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.024052
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02656
ELECTRON MICROSCOPYr_nbd_refined0.2050.2750
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1930.23651
ELECTRON MICROSCOPYr_nbtor_refined0.1730.21664
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0860.22225
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.2040.271
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0530.23
ELECTRON MICROSCOPYr_mcbond_it11.41512.2221908
ELECTRON MICROSCOPYr_mcbond_other11.41512.2221908
ELECTRON MICROSCOPYr_mcangle_it18.31418.3182357
ELECTRON MICROSCOPYr_mcangle_other18.31118.3222358
ELECTRON MICROSCOPYr_scbond_it9.39613.7131833
ELECTRON MICROSCOPYr_scbond_other9.39313.7161834
ELECTRON MICROSCOPYr_scangle_it16.79719.942695
ELECTRON MICROSCOPYr_scangle_other16.79419.9442696
ELECTRON MICROSCOPYr_lrange_it30.246234.79914036
ELECTRON MICROSCOPYr_lrange_other30.245234.80114037
ELECTRON MICROSCOPYr_ncsr_local_group_10.2210.052045
ELECTRON MICROSCOPYr_ncsr_local_group_20.2380.051979
ELECTRON MICROSCOPYr_ncsr_local_group_30.2260.051993
ELECTRON MICROSCOPYr_ncsr_local_group_40.2160.052049
ELECTRON MICROSCOPYr_ncsr_local_group_50.2210.052331
ELECTRON MICROSCOPYr_ncsr_local_group_60.2340.052248
ELECTRON MICROSCOPYr_ncsr_local_group_70.2280.052298
ELECTRON MICROSCOPYr_ncsr_local_group_80.2190.052302
ELECTRON MICROSCOPYr_ncsr_local_group_90.2120.052339
ELECTRON MICROSCOPYr_ncsr_local_group_100.2240.052249
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.220910.05005
12AELECTRON MICROSCOPYLocal ncs0.220910.05005
23AELECTRON MICROSCOPYLocal ncs0.238390.05005
24AELECTRON MICROSCOPYLocal ncs0.238390.05005
35AELECTRON MICROSCOPYLocal ncs0.225950.05005
36AELECTRON MICROSCOPYLocal ncs0.225950.05005
47AELECTRON MICROSCOPYLocal ncs0.215720.05006
48AELECTRON MICROSCOPYLocal ncs0.215720.05006
59AELECTRON MICROSCOPYLocal ncs0.220770.05005
510AELECTRON MICROSCOPYLocal ncs0.220770.05005
611AELECTRON MICROSCOPYLocal ncs0.233940.05005
612AELECTRON MICROSCOPYLocal ncs0.233940.05005
713AELECTRON MICROSCOPYLocal ncs0.228120.05005
714AELECTRON MICROSCOPYLocal ncs0.228120.05005
815AELECTRON MICROSCOPYLocal ncs0.219130.05005
816AELECTRON MICROSCOPYLocal ncs0.219130.05005
917AELECTRON MICROSCOPYLocal ncs0.21170.05006
918AELECTRON MICROSCOPYLocal ncs0.21170.05006
1019AELECTRON MICROSCOPYLocal ncs0.224160.05005
1020AELECTRON MICROSCOPYLocal ncs0.224160.05005
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
2.5-2.5650.78866560.78866560.0870.788
2.565-2.6350.81164250.81164250.0940.811
2.635-2.7120.77863210.77863210.0760.778
2.712-2.7950.74360730.74360730.0750.743
2.795-2.8860.70658910.70658910.1340.706
2.886-2.9880.64957480.64957480.1720.649
2.988-3.10.60455320.60455320.1720.604
3.1-3.2270.57752810.57752810.2090.577
3.227-3.370.53150360.53150360.310.531
3.37-3.5340.55448770.55448770.3420.554
3.534-3.7250.53445880.53445880.4690.534
3.725-3.9510.49243980.49243980.6090.492
3.951-4.2230.42541220.42541220.7420.425
4.223-4.5610.4238090.4238090.7880.42
4.561-4.9950.45235230.45235230.7990.452
4.995-5.5820.52732030.52732030.7570.527
5.582-6.4420.70527930.70527930.6030.705
6.442-7.880.52423550.52423550.6450.524
7.88-11.1030.45318390.45318390.7320.453
11.103-91.910.3710290.3710290.9070.37

+
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://pdbjlvh1.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