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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


centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / atrial cardiac muscle cell action potential / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / 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 / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Flemming body / SUMOylation of RNA binding proteins / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / centrosome cycle / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of programmed cell death / nucleocytoplasmic transport / positive regulation of epidermal growth factor receptor signaling pathway / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / PTB domain binding / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of DNA replication proteins / positive regulation of SMAD protein signal transduction / Regulation of HSF1-mediated heat shock response / mRNA transport / regulation of signal transduction / nuclear pore / protein targeting / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Hsp70 protein binding / positive regulation of mitotic nuclear division / regulation of mitotic spindle organization / SH2 domain binding / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / ubiquitin binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / phospholipid binding / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / spindle pole / mitotic spindle / cellular senescence / nuclear envelope / protein transport / signaling receptor complex adaptor activity / 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 / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / membrane / 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 Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III ...Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / 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, 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
  • Download
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8085.png

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.7 Å/pix.
x 144 pix.
= 964.8 Å		6.7 Å/pix.
x 144 pix.
= 964.8 Å		6.7 Å/pix.
x 144 pix.
= 964.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.7 Å
Density

Histogram

Histogram (log scale)
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

Histogram

Histogram (log scale)

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Mask #2

Fileemd_8085_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

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Image processing

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
ExtractionNumber tomograms: 101 / Number images used: 11112
Final angle assignmentType: OTHER

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