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- EMDB-0986: Cytoplasmic ring of the Xenopus laevis nuclear pore complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0986
TitleCytoplasmic ring of the Xenopus laevis nuclear pore complex
Map dataCR
Sample
  • Cell: Xenopus LaevisAfrican clawed frog
Biological speciesXenopus laevis (African clawed frog)
Methodsubtomogram averaging / cryo EM / Resolution: 9.1 Å
AuthorsLi S / Zhang YQ
CitationJournal: Cell Res / Year: 2020
Title: Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex.
Authors: Yanqing Zhang / Sai Li / Chao Zeng / Gaoxingyu Huang / Xuechen Zhu / Qifan Wang / Kunpeng Wang / Qiang Zhou / Chuangye Yan / Wusheng Zhang / Guangwen Yang / Minhao Liu / Qinghua Tao / Jianlin Lei / Yigong Shi /
Abstract: The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ...The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes and a Grid domain, which serves as a rigid base for the Finger domain. Two neighboring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighboring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.
History
DepositionJan 31, 2020-
Header (metadata) releaseMay 20, 2020-
Map releaseMay 20, 2020-
UpdateJun 10, 2020-
Current statusJun 10, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0986.png

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Map

FileDownload / File: emd_0986.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCR
Voxel sizeX=Y=Z: 2.222 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-16.5749 - 19.225092
Average (Standard dev.)0.038429327 (±0.93309724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 711.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2222.2222.222
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z711.040711.040711.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-16.57519.2250.038

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Supplemental data

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Sample components

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Entire : Xenopus Laevis

EntireName: Xenopus Laevis (African clawed frog)
Components
  • Cell: Xenopus LaevisAfrican clawed frog

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Supramolecule #1: Xenopus Laevis

SupramoleculeName: Xenopus Laevis / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5 / Component - Concentration: 1.6 M / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-8 / Average exposure time: 0.8 sec. / Average electron dose: 2.93 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 1425 / Number images used: 292232 / Software - Name: Dynamo (ver. 1.1.333)
CTF correctionSoftware: (Name: CTFFIND (ver. 4), NOVACTF)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: Dynamo (ver. 1.1.333) / Details: Sub-volume alignment
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.1.333) / Number subtomograms used: 112196

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Atomic model buiding 1

RefinementOverall B value: 1000

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