[English] 日本語
Yorodumi
- EMDB-5411: The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5411
TitleThe Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography
Map dataAveraged structure of the human nuclear pore complex asymmetric unit
Sample
  • Sample: Asymmetric unit of the human nuclear pore complex
  • Organelle or cellular component: nuclear pore complex
KeywordsCryo-electron tomography / human nuclear pore complex / nuclear envelope / nucleocytoplasmic transport
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 66.0 Å
AuthorsMaimon T / Elad N / Dahan I / Medalia O
CitationJournal: Structure / Year: 2012
Title: The human nuclear pore complex as revealed by cryo-electron tomography.
Authors: Tal Maimon / Nadav Elad / Idit Dahan / Ohad Medalia /
Abstract: Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, ...Nuclear pore complexes (NPCs) are the sole passage through the nuclear envelope, connecting the cytoplasm to the nucleoplasm. These gigantic molecular machines, over 100 MDa in molecular weight, allow free diffusion of small molecules and ions while mediating selective energy-dependent nucleocytoplasmic transport of large macromolecules. Here, we applied cryo-electron tomography to human fibroblast cells, reconstructing their nuclear envelopes without applying any purification steps. From these reconstructions, we extracted subtomograms containing individual NPCs and utilized in silico subtomogram averaging procedures to determine the structure of the mammalian pore complex at a resolution of ∼6.6 nm. Beyond revealing the canonical features of the human NPC, our analysis identified inner lateral channels and fusing bridge-like structures, suggesting alternative routes of peripheral nuclear passage. Finally, we concluded from our structural analysis that the human NPC is structurally distinct from that of lower eukaryotes in terms of dimension and organization but resembles its amphibian (frog) counterpart.
History
DepositionApr 7, 2012-
Header (metadata) releaseApr 17, 2013-
Map releaseApr 17, 2013-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.115
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5411.jpg

Downloads & links

-
Map

FileDownload / File: emd_5411.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged structure of the human nuclear pore complex asymmetric unit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.2 Å/pix.
x 128 pix.
= 1049.6 Å		8.2 Å/pix.
x 128 pix.
= 1049.6 Å		8.2 Å/pix.
x 128 pix.
= 1049.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115 / Movie #1: 0.115
Minimum - Maximum-0.37820762 - 0.48475263
Average (Standard dev.)0.00469575 (±0.07388216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 1049.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.28.28.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z1049.6001049.6001049.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.3780.4850.005

-
Supplemental data

-
Sample components

-
Entire : Asymmetric unit of the human nuclear pore complex

EntireName: Asymmetric unit of the human nuclear pore complex
Components
  • Sample: Asymmetric unit of the human nuclear pore complex
  • Organelle or cellular component: nuclear pore complex

-
Supramolecule #1000: Asymmetric unit of the human nuclear pore complex

SupramoleculeName: Asymmetric unit of the human nuclear pore complex / type: sample / ID: 1000
Oligomeric state: octamer (actual refined structure represents an asymmetric unit of the NPC)
Number unique components: 1

-
Supramolecule #1: nuclear pore complex

SupramoleculeName: nuclear pore complex / type: organelle_or_cellular_component / ID: 1 / Oligomeric state: octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: U2OS / Organelle: Nucleus / Location in cell: Nuclear envelope

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferDetails: Dulbecco phosphate buffer saline
GridDetails: 200 mesh gold grids, silicon coated
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: Blot for 4 seconds before plunging

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 90 K
Specialist opticsEnergy filter - Name: GIF2002
DateJan 1, 2010
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000
Sample stageSpecimen holder: nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Detailsmanual selection
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 66.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: TOM_toolbox_software_package / Number subtomograms used: 1696

+
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