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- EMDB-5151: Negative-stain 3D EM structure of the budding yeast Nup84 complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-5151
TitleNegative-stain 3D EM structure of the budding yeast Nup84 complex, straight-stem conformation.
Map dataMap of yeast Nup84 complex, "straight-stem" conformation
Sample
  • Sample: Nup84 complex isolated from budding yeast. This heptameric complex contains one copy each of Nup133, Nup84, Nup145C, Sec13, Nup85, Seh1 and Nup120.
  • Protein or peptide: Nup84 complex
KeywordsNuclear Pore complex / Nup84 complex / Nup107 complex
Biological speciesunidentified (others)
Methodsingle particle reconstruction / negative staining / Resolution: 35.0 Å
AuthorsKampmann M / Blobel G
CitationJournal: Nat Struct Mol Biol / Year: 2009
Title: Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex.
Authors: Martin Kampmann / Günter Blobel /
Abstract: The nuclear pore complex mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively known as nucleoporins. Nucleoporins are ...The nuclear pore complex mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively known as nucleoporins. Nucleoporins are organized into distinct subcomplexes. We optimized the isolation of a putative membrane-coating subcomplex of the nuclear pore complex, the heptameric Nup84 complex, and analyzed its structure by EM. Our data confirmed the previously reported 'Y' shape. We discerned additional structural details, including specific hinge regions at which the particle shows great flexibility. We determined the three-dimensional structures of two conformers, mapped the localization of two nucleoporins within the subcomplex and docked known crystal structures into the EM maps. The free ends of the Y-shaped particle are formed by beta-propellers; the connecting segments consist of alpha-solenoids. Notably, the same organizational principle is found in the clathrin triskelion, which may share a common evolutionary origin with the heptameric complex.
History
DepositionDec 13, 2009-
Header (metadata) releaseJan 6, 2010-
Map releaseJan 6, 2010-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.004
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5151.tiff

Downloads & links

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Map

FileDownload / File: emd_5151.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of yeast Nup84 complex, "straight-stem" conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.91 Å/pix.
x 112 pix.
= 661.92 Å		5.91 Å/pix.
x 112 pix.
= 661.92 Å		5.91 Å/pix.
x 112 pix.
= 661.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.004
Minimum - Maximum-0.009273 - 0.012926
Average (Standard dev.)-0.000033525 (±0.000615969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 661.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.915.915.91
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z661.920661.920661.920
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS112112112
D min/max/mean-0.0090.013-0.000

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Supplemental data

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Sample components

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Entire : Nup84 complex isolated from budding yeast. This heptameric comple...

EntireName: Nup84 complex isolated from budding yeast. This heptameric complex contains one copy each of Nup133, Nup84, Nup145C, Sec13, Nup85, Seh1 and Nup120.
Components
  • Sample: Nup84 complex isolated from budding yeast. This heptameric complex contains one copy each of Nup133, Nup84, Nup145C, Sec13, Nup85, Seh1 and Nup120.
  • Protein or peptide: Nup84 complex

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Supramolecule #1000: Nup84 complex isolated from budding yeast. This heptameric comple...

SupramoleculeName: Nup84 complex isolated from budding yeast. This heptameric complex contains one copy each of Nup133, Nup84, Nup145C, Sec13, Nup85, Seh1 and Nup120.
type: sample / ID: 1000 / Oligomeric state: heptamer / Number unique components: 1
Molecular weightTheoretical: 580 KDa

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Macromolecule #1: Nup84 complex

MacromoleculeName: Nup84 complex / type: protein_or_peptide / ID: 1 / Name.synonym: Nup84 complex / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 580 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 200 mM NaCl, 110 mM potassium acetate, 2 mM MgCl2, 20 mM HEPES (pH 7.5), 0.05% (w/v) CHAPS and 1 mM DTT
StainingType: NEGATIVE
Details: Grids with adsorbed complex were stained with three drops of 2% uranyl formate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2100
DateAug 1, 2008
Image recordingAverage electron dose: 10 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 40641 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 25000
Sample stageSpecimen holder: eucentric / Specimen holder model: JEOL / Tilt angle max: 50

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Image processing

CTF correctionDetails: none
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER, EMAN / Number images used: 4430

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