[English] 日本語
Yorodumi
- EMDB-3104: The human Nuclear Pore Complex with nucleoporin 358 knockdown -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3104
TitleThe human Nuclear Pore Complex with nucleoporin 358 knockdown
Map dataReconstruction of human nuclear pore complex after Nup358 knockdown
Sample
  • Sample: Human nuclear pore complex with nucleoporin 358 knockdown
  • Protein or peptide: nuclear pore complex
Keywordsnuclear pore complex / Nup358 knockdown
Function / homology
Function and homology information


GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading ...GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / atrial cardiac muscle cell action potential / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / lamellipodium assembly / neural tube development / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / female gonad development / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / mRNA transport / cellular response to nutrient levels / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of TORC1 signaling / neurogenesis / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of TORC1 signaling / serine-type peptidase activity / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to amino acid starvation / nuclear periphery / SUMOylation of chromatin organization proteins / HCMV Late Events / chromosome segregation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / molecular condensate scaffold activity / kinetochore / ISG15 antiviral mechanism / spindle / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / protein transport / actin cytoskeleton / snRNP Assembly / nuclear membrane / transcription coactivator activity / defense response to Gram-positive bacterium
Similarity search - Function
: / : / : / Nucleoporin NUP160, helical domain / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup85-like ...: / : / : / Nucleoporin NUP160, helical domain / Nup160 C-terminal TPR / NUP160/120 middle TPR / Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nup98, Gle2-binding sequence / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / 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 / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup155 / Nuclear pore complex protein Nup98-Nup96 / Protein SEC13 homolog / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup160 / Nucleoporin Nup43 / Nucleoporin Nup37 / Nuclear pore complex protein Nup133 / Nucleoporin SEH1 / Nuclear pore complex protein Nup85
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 37.5 Å
Authorsvon Appen A / Kosinski J / Sparks L / Ori A / DiGuilio A / Vollmer B / Mackmull M / Banterle N / Parca L / Kastritis P ...von Appen A / Kosinski J / Sparks L / Ori A / DiGuilio A / Vollmer B / Mackmull M / Banterle N / Parca L / Kastritis P / Buczak K / Mosalaganti S / Hagen W / Andres-Pons A / Lemke EA / Bork P / Antonin W / Glavy JS / Bui KH / Beck M
CitationJournal: Nature / Year: 2015
Title: In situ structural analysis of the human nuclear pore complex.
Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / ...Authors: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / Katarzyna Buczak / Shyamal Mosalaganti / Wim Hagen / Amparo Andres-Pons / Edward A Lemke / Peer Bork / Wolfram Antonin / Joseph S Glavy / Khanh Huy Bui / Martin Beck /
Abstract: Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and ...Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.
History
DepositionJul 21, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseSep 30, 2015-
UpdateOct 7, 2015-
Current statusOct 7, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3104.png

Downloads & links

-
Map

FileDownload / File: emd_3104.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of human nuclear pore complex after Nup358 knockdown
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.6 Å/pix.
x 168 pix.
= 1444.8 Å		8.6 Å/pix.
x 168 pix.
= 1444.8 Å		8.6 Å/pix.
x 168 pix.
= 1444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-11.19243908 - 19.80205917
Average (Standard dev.)-0.00104026 (±1.6228081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 1444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.68.68.6
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z1444.8001444.8001444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-800-4
NX/NY/NZ1611358
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-11.19219.802-0.001

-
Supplemental data

-
Sample components

-
Entire : Human nuclear pore complex with nucleoporin 358 knockdown

EntireName: Human nuclear pore complex with nucleoporin 358 knockdown
Components
  • Sample: Human nuclear pore complex with nucleoporin 358 knockdown
  • Protein or peptide: nuclear pore complex

-
Supramolecule #1000: Human nuclear pore complex with nucleoporin 358 knockdown

SupramoleculeName: Human nuclear pore complex with nucleoporin 358 knockdown
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 120 MDa / Theoretical: 120 MDa

-
Macromolecule #1: nuclear pore complex

MacromoleculeName: nuclear pore complex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus / Location in cell: Nuclear envelope

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 20mM Tris, 0.2-0.4% Trehalose
GridDetails: 200 mesh Quantifoil Copper Holey Carbon Grid R2/1
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateSep 20, 2014
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Average electron dose: 100 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 34883 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 19500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -44 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsThe subtomograms were selected manually and further processed by iterative, symmetry-independent averaging.
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.5 Å / Resolution method: OTHER / Software - Name: IMOD, TOM, AV3 / Number subtomograms used: 7360

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more