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- PDB-7n84: Double nuclear outer ring from the isolated yeast NPC -

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Basic information

Entry
Database: PDB / ID: 7n84
TitleDouble nuclear outer ring from the isolated yeast NPC
Components
  • Nucleoporin 145c
  • Nucleoporin NUP120
  • Nucleoporin NUP133
  • Nucleoporin NUP188
  • Nucleoporin NUP84
  • Nucleoporin NUP85
  • Nucleoporin SEH1
  • Protein transport protein SEC13
  • unknown
KeywordsTRANSLOCASE / nuclear pore complex / outer ring / Nup84 complex
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore inner ring / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization ...mRNA export from nucleus in response to heat stress / nuclear pore inner ring / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / COPII-mediated vesicle transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore localization / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / regulation of TORC1 signaling / nuclear pore organization / nuclear pore outer ring / telomere tethering at nuclear periphery / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / positive regulation of protein exit from endoplasmic reticulum / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / tRNA export from nucleus / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / vacuolar membrane / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / subtelomeric heterochromatin formation / mRNA transport / mRNA export from nucleus / nuclear pore / ERAD pathway / protein export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / cell periphery / protein import into nucleus / double-strand break repair / protein transport / nuclear envelope / cellular response to heat / nuclear membrane / chromosome, telomeric region / hydrolase activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleoporin NUP120, helical domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup85-like / Nucleoporin Nup120/160 ...Nucleoporin NUP120, helical domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Sec13/Seh1 family / 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 peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP120 / Nucleoporin NUP133 / Nucleoporin NUP85 / Nucleoporin NUP145 / Nucleoporin NUP188 / Nucleoporin NUP84 / Nucleoporin SEH1 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.6 Å
Model detailsyeast Nup84 complexes in double outer ring
AuthorsAkey, C.W. / Rout, M.P. / Ouch, C. / Echevarria, I. / Fernandez-Martinez, J. / Nudelman, I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM45377 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM112108 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM109824 United States
CitationJournal: Cell / Year: 2022
Title: Comprehensive structure and functional adaptations of the yeast nuclear pore complex.
Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / ...Authors: Christopher W Akey / Digvijay Singh / Christna Ouch / Ignacia Echeverria / Ilona Nudelman / Joseph M Varberg / Zulin Yu / Fei Fang / Yi Shi / Junjie Wang / Daniel Salzberg / Kangkang Song / Chen Xu / James C Gumbart / Sergey Suslov / Jay Unruh / Sue L Jaspersen / Brian T Chait / Andrej Sali / Javier Fernandez-Martinez / Steven J Ludtke / Elizabeth Villa / Michael P Rout /
Abstract: Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub- ...Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.
History
DepositionJun 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure viewerMolecule:
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Assembly

Deposited unit
X: Nucleoporin NUP188
Y: unknown
Z: unknown
a: Nucleoporin NUP120
b: Nucleoporin NUP85
c: Nucleoporin 145c
d: Protein transport protein SEC13
e: Nucleoporin SEH1
f: Nucleoporin NUP84
g: Nucleoporin NUP133
l: Nucleoporin NUP120
m: Nucleoporin NUP85
n: Nucleoporin 145c
o: Protein transport protein SEC13
p: Nucleoporin SEH1
q: Nucleoporin NUP84
r: Nucleoporin NUP133


Theoretical massNumber of molelcules
Total (without water)1,351,74417
Polymers1,351,74417
Non-polymers00
Water00
1
X: Nucleoporin NUP188
Y: unknown
Z: unknown
a: Nucleoporin NUP120
b: Nucleoporin NUP85
c: Nucleoporin 145c
d: Protein transport protein SEC13
e: Nucleoporin SEH1
f: Nucleoporin NUP84
g: Nucleoporin NUP133
l: Nucleoporin NUP120
m: Nucleoporin NUP85
n: Nucleoporin 145c
o: Protein transport protein SEC13
p: Nucleoporin SEH1
q: Nucleoporin NUP84
r: Nucleoporin NUP133
x 8


Theoretical massNumber of molelcules
Total (without water)10,813,954136
Polymers10,813,954136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C8 (8 fold cyclic))

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Components

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Protein , 9 types, 17 molecules XYZalbmcndoepfqgr

#1: Protein Nucleoporin NUP188 / Nuclear pore protein NUP188


Mass: 188753.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52593
#2: Protein unknown


Mass: 5379.623 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#3: Protein Nucleoporin NUP120 / Nuclear pore protein NUP120


Mass: 120560.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P35729
#4: Protein Nucleoporin NUP85 / Nuclear pore protein NUP85


Mass: 84972.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46673
#5: Protein Nucleoporin 145c


Mass: 81157.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49687
#6: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04491
#7: Protein Nucleoporin SEH1 / Nuclear pore protein SEH1 / SEC13 homolog 1


Mass: 39170.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53011
#8: Protein Nucleoporin NUP84 / Nuclear pore protein NUP84


Mass: 83718.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52891
#9: Protein Nucleoporin NUP133 / Nuclear pore protein NUP133


Mass: 133452.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36161

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Details

Compound detailsNup84 complex with Nup188 and basket anchor

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: yeast double outer ring / Type: COMPLEX
Details: Novel outer ring C8 protomer with two copies of Nup84 complex, one copy of Nup188 and an unknown basket anchor model
Entity ID: all / Source: NATURAL
Molecular weightValue: 10.4 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Cellular location: nuclear envelope
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
250 mMpotassium acetate1
320 mMsodium chlorideNaCl1
42 mMmagnesium chloride1
51 mMDTT1
60.1 percent wt/wtDeoxyBigChaps1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: double outer ring imaged from isolated yeast NPC
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 37651 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4015
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 2-40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.18CTF correction
7UCSF Chimera1.14model fitting
9RELION2initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13VMD1.9.3model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 11.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Algorithm: FOURIER SPACE / Details: gold standard in RELION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: molecular dynamics flexible fitting

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