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- EMDB-8085: Sub-unit of the Inner ring of the Nuclear Pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-8085
TitleSub-unit of the Inner ring of the Nuclear Pore complex
Map dataNone
Sample
  • Complex: Inner ring of the Nuclear Pore complex
Function / homology
Function and homology information


positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel ...positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / nuclear pore organization / nuclear pore complex assembly / atrial cardiac muscle cell action potential / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / negative regulation of programmed cell death / mitotic centrosome separation / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / nuclear localization sequence binding / PTB domain binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / negative regulation of epidermal growth factor receptor signaling pathway / Vpr-mediated nuclear import of PICs / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / protein targeting / mRNA transport / regulation of signal transduction / SUMOylation of DNA damage response and repair proteins / mRNA export from nucleus / nuclear pore / regulation of mitotic spindle organization / nuclear periphery / SUMOylation of chromatin organization proteins / Hsp70 protein binding / positive regulation of mitotic nuclear division / HCMV Late Events / ubiquitin binding / SH2 domain binding / phospholipid binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / ISG15 antiviral mechanism / spindle pole / HCMV Early Events / mitotic spindle / protein import into nucleus / protein transport / signaling receptor complex adaptor activity / cellular senescence / nuclear envelope / snRNP Assembly / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / chromatin binding / protein-containing complex binding / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / nucleoplasm / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, Nup155-like, C-terminal, subdomain 3 ...Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin NSP1/NUP62 / Nucleoporin Nup188 / Nsp1-like C-terminal region / Nucleoporin complex subunit 54 / 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 interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Armadillo-type fold
Similarity search - Domain/homology
Nuclear pore complex protein Nup155 / Nuclear pore glycoprotein p62 / Nucleoporin NUP188 / Nucleoporin p54 / Nuclear pore complex protein Nup93 / Nuclear pore complex protein Nup205 / Nucleoporin p58/p45
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 21.4 Å
AuthorsMosalaganti S
CitationJournal: Science / Year: 2016
Title: Molecular architecture of the inner ring scaffold of the human nuclear pore complex.
Authors: Jan Kosinski / Shyamal Mosalaganti / Alexander von Appen / Roman Teimer / Amanda L DiGuilio / William Wan / Khanh Huy Bui / Wim J H Hagen / John A G Briggs / Joseph S Glavy / Ed Hurt / Martin Beck /
Abstract: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these ...Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.
History
DepositionFeb 22, 2016-
Header (metadata) releaseApr 27, 2016-
Map releaseApr 27, 2016-
UpdateApr 11, 2018-
Current statusApr 11, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 36.6
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 36.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ijn
  • Surface level: 36.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ijo
  • Surface level: 36.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5ijo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8085.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 6.7 Å
Density
Contour LevelBy AUTHOR: 36.600000000000001 / Movie #1: 36.6
Minimum - Maximum0. - 315.784240000000011
Average (Standard dev.)1.3284056 (±10.659494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin349435
Dimensions144144144
Spacing144144144
CellA=B=C: 964.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.76.76.7
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z964.800964.800964.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS943435
NC/NR/NS144144144
D min/max/mean0.000315.7841.328

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Supplemental data

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Mask #1

Fileemd_8085_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Mask #2

Fileemd_8085_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Inner ring of the Nuclear Pore complex

EntireName: Inner ring of the Nuclear Pore complex
Components
  • Complex: Inner ring of the Nuclear Pore complex

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Supramolecule #1: Inner ring of the Nuclear Pore complex

SupramoleculeName: Inner ring of the Nuclear Pore complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HeLa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 101 / Number images used: 11112
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 8400

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