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- EMDB-2026: Structure of the proteasome subunit Rpn1 -

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Basic information

Entry
Database: EMDB / ID: 2026
TitleStructure of the proteasome subunit Rpn1
Keywordsproteasome / rpn1 / 19S subunit
SampleRpn1
SourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Map dataMap of the proteasome subunit Rpn1 from S. cerevisiae
Methodsingle particle reconstruction, at 25 A resolution
AuthorsHe J / Kulkarni K / daFonseca P / Krutauz D / Glickman M / Barford D / Morris E
CitationStructure, 2012, 20, 513-521

Structure, 2012, 20, 513-521 StrPapers
The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings.
Jun He / Kiran Kulkarni / Paula C A da Fonseca / Dasha Krutauz / Michael H Glickman / David Barford / Edward P Morris

DateDeposition: Jan 9, 2012 / Header (metadata) release: Jan 20, 2012 / Map release: Apr 13, 2012 / Last update: Jan 9, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 5.5
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_2026.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.17 A/pix
= 278.144 A
128 pix
2.17 A/pix
= 278.144 A
128 pix
2.17 A/pix
= 278.144 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.173 A
Density
Contour Level:5.5 (by author), 5.5 (movie #1):
Minimum - Maximum-11.30645084 - 36.75227737
Average (Standard dev.)0E-8 (1.00000012)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 278.144 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.1732.1732.173
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z278.144278.144278.144
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-11.30636.752-0.000

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Supplemental data

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Sample components

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Entire Rpn1

EntireName: Rpn1 / Number of components: 1
MassTheoretical: 109.492 kDa

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Component #1: protein, Rpn1

ProteinName: Rpn1 / a.k.a: Rpn1 / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 109.492 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml
Support filmCarbon film on quantifoil
Staining2% uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 800 - 900 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 71 / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: Imagic / Resolution: 25 A / Resolution method: FSC 0.5

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