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- PDB-7n85: Inner ring spoke from the isolated yeast NPC -

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Basic information

Entry
Database: PDB / ID: 7n85
TitleInner ring spoke from the isolated yeast NPC
Components
  • Nucleoporin ASM4
  • Nucleoporin NIC96
  • Nucleoporin NSP1
  • Nucleoporin NUP157
  • Nucleoporin NUP170
  • Nucleoporin NUP188
  • Nucleoporin NUP192
  • Nucleoporin NUP49/NSP49
  • Nucleoporin NUP53
  • Nucleoporin NUP57
  • Unknown connectors
KeywordsTRANSLOCASE / nuclear pore complex / inner ring / spoke
Function / homology
Function and homology information


response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of nucleocytoplasmic transport ...response to spindle checkpoint signaling / nuclear pore linkers / regulation of protein desumoylation / mRNA export from nucleus in response to heat stress / nuclear pore inner ring / protein localization to nuclear inner membrane / chromosome, subtelomeric region / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / regulation of nucleocytoplasmic transport / nuclear pore organization / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / tRNA export from nucleus / SUMOylation of SUMOylation proteins / protein localization to kinetochore / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / regulation of mitotic nuclear division / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / chromosome segregation / promoter-specific chromatin binding / molecular condensate scaffold activity / heterochromatin formation / phospholipid binding / protein import into nucleus / protein transport / nuclear envelope / single-stranded DNA binding / nuclear membrane / amyloid fibril formation / cell division / chromatin binding / protein-containing complex binding / positive regulation of DNA-templated transcription / DNA binding / RNA binding / identical protein binding / nucleus
Similarity search - Function
RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 ...RNA-recognition motif (RRM) Nup35-type domain / Nucleoporin, NUP53 / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin Nup188 / : / Nucleoporin complex subunit 54 / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin FG repeat / Nucleoporin FG repeat region / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Nucleoporin NSP1 / Nucleoporin NIC96 / Nucleoporin NUP170 / Nucleoporin NUP157 / Nucleoporin NUP192 / Nucleoporin NUP57 / Nucleoporin NUP188 / Nucleoporin NUP49/NSP49 / Nucleoporin NUP53 / Nucleoporin ASM4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 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 visualization

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Assembly

Deposited unit
0: Nucleoporin NUP170
1: Nucleoporin NUP157
5: Unknown connectors
6: Unknown connectors
A: Nucleoporin NSP1
B: Nucleoporin NUP57
C: Nucleoporin NUP49/NSP49
D: Nucleoporin NSP1
E: Nucleoporin NUP57
F: Nucleoporin NUP49/NSP49
G: Nucleoporin NSP1
H: Nucleoporin NUP57
I: Nucleoporin NUP49/NSP49
J: Nucleoporin NSP1
K: Nucleoporin NUP57
L: Nucleoporin NUP49/NSP49
M: Nucleoporin NUP192
N: Nucleoporin NUP188
O: Nucleoporin NUP192
P: Nucleoporin NUP188
Q: Nucleoporin NIC96
R: Nucleoporin NIC96
S: Nucleoporin NIC96
T: Nucleoporin NIC96
U: Nucleoporin NUP53
V: Nucleoporin ASM4
W: Nucleoporin NUP53
X: Nucleoporin ASM4
Y: Nucleoporin NUP170
Z: Nucleoporin NUP157


Theoretical massNumber of molelcules
Total (without water)2,801,65130
Polymers2,801,65130
Non-polymers00
Water00
1
0: Nucleoporin NUP170
1: Nucleoporin NUP157
5: Unknown connectors
6: Unknown connectors
A: Nucleoporin NSP1
B: Nucleoporin NUP57
C: Nucleoporin NUP49/NSP49
D: Nucleoporin NSP1
E: Nucleoporin NUP57
F: Nucleoporin NUP49/NSP49
G: Nucleoporin NSP1
H: Nucleoporin NUP57
I: Nucleoporin NUP49/NSP49
J: Nucleoporin NSP1
K: Nucleoporin NUP57
L: Nucleoporin NUP49/NSP49
M: Nucleoporin NUP192
N: Nucleoporin NUP188
O: Nucleoporin NUP192
P: Nucleoporin NUP188
Q: Nucleoporin NIC96
R: Nucleoporin NIC96
S: Nucleoporin NIC96
T: Nucleoporin NIC96
U: Nucleoporin NUP53
V: Nucleoporin ASM4
W: Nucleoporin NUP53
X: Nucleoporin ASM4
Y: Nucleoporin NUP170
Z: Nucleoporin NUP157
x 8


Theoretical massNumber of molelcules
Total (without water)22,413,209240
Polymers22,413,209240
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 , 10 types, 28 molecules 0Y1ZADGJBEHKCFILMONPQRSTUWVX

#1: Protein Nucleoporin NUP170 / Nuclear pore protein NUP170


Mass: 169651.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38181
#2: Protein Nucleoporin NUP157 / Nuclear pore protein NUP157


Mass: 156827.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40064
#4: Protein
Nucleoporin NSP1 / Nuclear pore protein NSP1 / Nucleoskeletal-like protein / p110


Mass: 86611.672 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14907
#5: Protein
Nucleoporin NUP57 / Nuclear pore protein NUP57


Mass: 57547.145 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P48837
#6: Protein
Nucleoporin NUP49/NSP49 / Nuclear pore protein NUP49/NSP49


Mass: 49174.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02199
#7: Protein Nucleoporin NUP192 / Nuclear pore protein NUP192


Mass: 191718.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47054
#8: Protein Nucleoporin NUP188 / Nuclear pore protein NUP188


Mass: 188753.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P52593
#9: Protein
Nucleoporin NIC96 / 96 kDa nucleoporin-interacting component / Nuclear pore protein NIC96


Mass: 96291.586 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34077
#10: Protein Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 52688.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03790
#11: Protein Nucleoporin ASM4 / Nuclear pore protein NUP59


Mass: 58853.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q05166

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Protein/peptide , 1 types, 2 molecules 56

#3: Protein/peptide Unknown connectors


Mass: 3081.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Details

Compound detailsspoke model

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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: spoke from yeast inner ring / Type: COMPLEX
Details: recombined inner ring from spoke multi-body and focused 3D refinements with isolated NPC
Entity ID: all / Source: NATURAL
Molecular weightValue: 16.0 MDa / Experimental value: YES
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: inner ring spoke 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 Chimeramodel 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: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145000 / Algorithm: FOURIER SPACE
Details: 1.5x spoke from multibody and focused refinements after re-extraction of particles
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: initial spoke model from PDBDEV_00000012, rigid body dock with chimera and fitting with MDFF

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