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- PDB-7q64: Cryo-em structure of the Nup98 fibril polymorph 1 -

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Basic information

Entry
Database: PDB / ID: 7q64
TitleCryo-em structure of the Nup98 fibril polymorph 1
ComponentsNuclear pore complex protein Nup98Nuclear pore
KeywordsPROTEIN FIBRIL / Nuclear pore complex protein Nup98 functional amyloid fibril PROTEIN FIBRIL
Function / homology
Function and homology information


telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore complex assembly / nuclear pore outer ring / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...telomere tethering at nuclear periphery / nuclear pore organization / nuclear pore complex assembly / nuclear pore outer ring / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / positive regulation of mRNA splicing, via spliceosome / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / nuclear periphery / serine-type peptidase activity / SUMOylation of chromatin organization proteins / HCMV Late Events / RHO GTPases Activate Formins / promoter-specific chromatin binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsIbanez de Opakua, A. / Geraets, J.A. / Frieg, B. / Dienemann, C. / Savastano, A. / Rankovic, M. / Cima-Omori, M.-S. / Schroeder, G.F. / Zweckstetter, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)787679 Germany
German Research Foundation (DFG)656281 Germany
CitationJournal: Nat Chem / Year: 2022
Title: Molecular interactions of FG nucleoporin repeats at high resolution.
Authors: Alain Ibáñez de Opakua / James A Geraets / Benedikt Frieg / Christian Dienemann / Adriana Savastano / Marija Rankovic / Maria-Sol Cima-Omori / Gunnar F Schröder / Markus Zweckstetter /
Abstract: Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear ...Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG-FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities.
History
DepositionNov 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup98
a: Nuclear pore complex protein Nup98
b: Nuclear pore complex protein Nup98
c: Nuclear pore complex protein Nup98
d: Nuclear pore complex protein Nup98
B: Nuclear pore complex protein Nup98
C: Nuclear pore complex protein Nup98
D: Nuclear pore complex protein Nup98
E: Nuclear pore complex protein Nup98
F: Nuclear pore complex protein Nup98
G: Nuclear pore complex protein Nup98
H: Nuclear pore complex protein Nup98
I: Nuclear pore complex protein Nup98
J: Nuclear pore complex protein Nup98
K: Nuclear pore complex protein Nup98
L: Nuclear pore complex protein Nup98
M: Nuclear pore complex protein Nup98
N: Nuclear pore complex protein Nup98
O: Nuclear pore complex protein Nup98
P: Nuclear pore complex protein Nup98
Q: Nuclear pore complex protein Nup98
R: Nuclear pore complex protein Nup98
S: Nuclear pore complex protein Nup98
T: Nuclear pore complex protein Nup98
U: Nuclear pore complex protein Nup98
V: Nuclear pore complex protein Nup98
W: Nuclear pore complex protein Nup98
X: Nuclear pore complex protein Nup98
Y: Nuclear pore complex protein Nup98
Z: Nuclear pore complex protein Nup98


Theoretical massNumber of molelcules
Total (without water)120,15630
Polymers120,15630
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 86 through 121)
d_2ens_1chain "B"
d_3ens_1(chain "D" and resid 86 through 121)
d_4ens_1chain "E"
d_5ens_1(chain "G" and resid 86 through 121)
d_6ens_1chain "H"
d_7ens_1(chain "J" and resid 86 through 121)
d_8ens_1chain "K"
d_9ens_1(chain "M" and resid 86 through 121)
d_10ens_1chain "N"
d_11ens_1(chain "P" and resid 86 through 121)
d_12ens_1chain "Q"
d_13ens_1(chain "S" and resid 86 through 121)
d_14ens_1chain "T"
d_15ens_1(chain "V" and resid 86 through 121)
d_16ens_1chain "W"
d_17ens_1(chain "Y" and resid 86 through 121)
d_18ens_1chain "Z"
d_19ens_1(chain "b" and resid 86 through 121)
d_20ens_1chain "D"
d_1ens_2chain "C"
d_2ens_2chain "F"
d_3ens_2chain "I"
d_4ens_2chain "L"
d_5ens_2chain "O"
d_6ens_2chain "R"
d_7ens_2chain "U"
d_8ens_2chain "X"
d_9ens_2chain "a"
d_10ens_2chain "d"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLYA2 - 37
d_21ens_1GLYGLYF1 - 36
d_31ens_1GLYGLYH2 - 37
d_41ens_1GLYGLYI1 - 36
d_51ens_1GLYGLYK2 - 37
d_61ens_1GLYGLYL1 - 36
d_71ens_1GLYGLYN2 - 37
d_81ens_1GLYGLYO1 - 36
d_91ens_1GLYGLYQ2 - 37
d_101ens_1GLYGLYR1 - 36
d_111ens_1GLYGLYT2 - 37
d_121ens_1GLYGLYU1 - 36
d_131ens_1GLYGLYW2 - 37
d_141ens_1GLYGLYX1 - 36
d_151ens_1GLYGLYZ2 - 37
d_161ens_1GLYGLYW1 - 36
d_171ens_1GLYGLYY2 - 37
d_181ens_1GLYGLYZ1 - 36
d_191ens_1GLYGLYC2 - 37
d_201ens_1GLYGLYD1 - 36
d_11ens_2ALAGLYG1 - 34
d_21ens_2ALAGLYJ1 - 34
d_31ens_2ALAGLYM1 - 34
d_41ens_2ALAGLYP1 - 34
d_51ens_2ALAGLYS1 - 34
d_61ens_2ALAGLYV1 - 34
d_71ens_2ALAGLYY1 - 34
d_81ens_2ALAGLYX1 - 34
d_91ens_2ALAGLYB1 - 34
d_101ens_2ALAGLYE1 - 34

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein/peptide ...
Nuclear pore complex protein Nup98 / Nuclear pore


Mass: 4005.211 Da / Num. of mol.: 30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP98, ADAR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52948

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: The nuclear pore complex protein Nup98 fibril polymorph 1
Type: COMPLEX
Details: The Nup98 polymorph 1 fibril is formed by three protofilaments, consisting of Nup98 monomers.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 2.557 sec. / Electron dose: 41 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4180

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
12RELION3.13D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.09 ° / Axial rise/subunit: 4.65 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 356482
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71697 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 28.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01417960
ELECTRON MICROSCOPYf_angle_d1.343610760
ELECTRON MICROSCOPYf_chiral_restr0.08911190
ELECTRON MICROSCOPYf_plane_restr0.00591460
ELECTRON MICROSCOPYf_dihedral_angle_d10.19892510
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints1.11008214431
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.197269271833
ens_1d_4AELECTRON MICROSCOPYNCS constraints1.11005824362
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.197217463967
ens_1d_6AELECTRON MICROSCOPYNCS constraints1.11007631936
ens_1d_7AELECTRON MICROSCOPYNCS constraints0.197225981256
ens_1d_8AELECTRON MICROSCOPYNCS constraints1.1100536066
ens_1d_9AELECTRON MICROSCOPYNCS constraints0.197220899053
ens_1d_10AELECTRON MICROSCOPYNCS constraints1.11006378353
ens_1d_11AELECTRON MICROSCOPYNCS constraints0.197224582031
ens_1d_12AELECTRON MICROSCOPYNCS constraints1.11006659516
ens_1d_13AELECTRON MICROSCOPYNCS constraints0.197256295386
ens_1d_14AELECTRON MICROSCOPYNCS constraints1.11005195854
ens_1d_15AELECTRON MICROSCOPYNCS constraints0.197211784802
ens_1d_16AELECTRON MICROSCOPYNCS constraints1.1100771498
ens_1d_17AELECTRON MICROSCOPYNCS constraints0.197251735376
ens_1d_18AELECTRON MICROSCOPYNCS constraints1.11008703117
ens_1d_19AELECTRON MICROSCOPYNCS constraints0.276154931977
ens_1d_20AELECTRON MICROSCOPYNCS constraints1.11007545787
ens_2d_2GELECTRON MICROSCOPYNCS constraints0.000668844920366
ens_2d_3GELECTRON MICROSCOPYNCS constraints0.000628100882646
ens_2d_4GELECTRON MICROSCOPYNCS constraints0.00069517054433
ens_2d_5GELECTRON MICROSCOPYNCS constraints0.00062034365446
ens_2d_6GELECTRON MICROSCOPYNCS constraints0.00047590335746
ens_2d_7GELECTRON MICROSCOPYNCS constraints0.000598797711097
ens_2d_8GELECTRON MICROSCOPYNCS constraints0.000618122041302
ens_2d_9GELECTRON MICROSCOPYNCS constraints0.000629753209705
ens_2d_10GELECTRON MICROSCOPYNCS constraints0.000641090283248

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