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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 / 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 ...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 / 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 / protein localization to nuclear inner membrane / nuclear pore organization / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / mitotic centrosome separation / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / Flemming body / Transport of Mature mRNA Derived from an Intronless Transcript / NS1 Mediated Effects on Host Pathways / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / NLS-bearing protein import into nucleus / centrosome cycle / nucleocytoplasmic transport / nuclear localization sequence binding / negative regulation of programmed cell death / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / PTB domain binding / 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 signal transduction / nuclear pore / Regulation of HSF1-mediated heat shock response / mitotic metaphase chromosome alignment / mRNA transport / SUMOylation of DNA damage response and repair proteins / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitotic nuclear division / nuclear periphery / SH2 domain binding / Hsp70 protein binding / SUMOylation of chromatin organization proteins / regulation of mitotic spindle organization / HCMV Late Events / ubiquitin binding / protein import into nucleus / Hsp90 protein binding / phospholipid binding / ISG15 antiviral mechanism / mitotic spindle / spindle pole / HCMV Early Events / nuclear envelope / protein transport / nuclear membrane / signaling receptor complex adaptor activity / snRNP Assembly / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / negative regulation of cell population proliferation / ribonucleoprotein complex / centrosome / chromatin binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 Nup188, N-terminal / Nucleoporin p58/p45 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup188 ...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, N-terminal subdomain III / Nucleoporin Nup188 / 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 interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / 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:
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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