[English] 日本語
Yorodumi
- EMDB-2445: Cryo-electron tomography of the human Nuclear Pore Complex with n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2445
TitleCryo-electron tomography of the human Nuclear Pore Complex with nucleoporin 214 knockdown
Map dataReconstruction of the human nuclear pore complex with nucleoporin 214 knockdown.
Sample
  • Sample: Human Nuclear Pore Complex with nucleoporin 214 Knockdown
  • Protein or peptide: Nuclear Pore ComplexNuclear pore
Keywordsnuclear pore complex / Nup214 knockdown
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / Resolution: 39.0 Å
AuthorsBui KH / von Appen A / DiGuilio AL / Ori A / Sparks L / Mackmull MT / Bock T / Hagen W / Andres-Pons A / Glavy JS / Beck M
CitationJournal: Cell / Year: 2013
Title: Integrated structural analysis of the human nuclear pore complex scaffold.
Authors: Khanh Huy Bui / Alexander von Appen / Amanda L DiGuilio / Alessandro Ori / Lenore Sparks / Marie-Therese Mackmull / Thomas Bock / Wim Hagen / Amparo Andrés-Pons / Joseph S Glavy / Martin Beck /
Abstract: The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 ...The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.
History
DepositionAug 22, 2013-
Header (metadata) releaseSep 25, 2013-
Map releaseDec 11, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2445.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the human nuclear pore complex with nucleoporin 214 knockdown.
Voxel sizeX=Y=Z: 8.6 Å
Density
Contour LevelBy AUTHOR: 2.3 / Movie #1: 2.3
Minimum - Maximum-11.12563705 - 19.53686905
Average (Standard dev.)-0.00046708 (±1.62281024)
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/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-11.12619.537-0.000

-
Supplemental data

-
Sample components

-
Entire : Human Nuclear Pore Complex with nucleoporin 214 Knockdown

EntireName: Human Nuclear Pore Complex with nucleoporin 214 Knockdown
Components
  • Sample: Human Nuclear Pore Complex with nucleoporin 214 Knockdown
  • Protein or peptide: Nuclear Pore ComplexNuclear pore

-
Supramolecule #1000: Human Nuclear Pore Complex with nucleoporin 214 Knockdown

SupramoleculeName: Human Nuclear Pore Complex with nucleoporin 214 Knockdown
type: sample / ID: 1000
Details: The sample is purified human nuclear envelope containing nuclear pore complex.
Number unique components: 1
Molecular weightMethod: Absolute Quantitative Mass Spectrometry

-
Macromolecule #1: Nuclear Pore Complex

MacromoleculeName: Nuclear Pore Complex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Nucleus / Location in cell: Nuclear pore complex
Molecular weightExperimental: 120 MDa / Theoretical: 120 MDa

-
Experimental details

-
Structure determination

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: NONE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 34883 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 19500
Specialist opticsEnergy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateSep 20, 2012
Image recordingCategory: CCD / Film or detector model: GATAN MULTISCAN / Average electron dose: 100 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, TOM, AV3 / Number subtomograms used: 4700
DetailsThe subtomograms were picked manually and further processed iterative symmetry independent averaging.

+
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