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Structure of the proteasome subunit Rpn1

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 5.5, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 5.5, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2026
TitleStructure of the proteasome subunit Rpn1
MapMap of the proteasome subunit Rpn1 from S. cerevisiae
SampleRpn1
Keywordsproteasome, rpn1, 19S subunit
AuthorsHe J, Kulkarni K, daFonseca P, Krutauz D, Glickman M, Barford D, Morris E
DateDeposition: 2012-01-09, Header release: 2012-01-20, Map release: 2012-04-13, Last update: 2012-04-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 5.5, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 5.5, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleStructure, Vol. 20, Issue 3, Page 513-21, Year 2012
TitleThe structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings.
AuthorsJun He, Kiran Kulkarni, Paula C A da Fonseca, Dasha Krutauz, Michael H Glickman, David Barford, Edward P Morris
Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom.
KeywordsAmino Acid Sequence, Models, Molecular, Molecular Sequence Data, Proteasome Endopeptidase Complex (chemistry, 3.4.25.1), Protein Conformation, RPN2 protein, human (2.4.1.119), Sequence Alignment, Tandem Repeat Sequences (genetics), Ubiquitin (metabolism)
LinksPII: S0969-2126(12)00021-4, DOI: 10.1016/j.str.2011.12.015, PubMed: 22405010
Map
Fileemd_2026.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.173 A/pix
= 278.144 A
128 pix
2.173 A/pix
= 278.144 A
128 pix
2.173 A/pix
= 278.144 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:5.5 (by author), 5.5 (movie #1):
Minimum - Maximum: -11.30645084 - 36.75227737
Average (Standard dev.): 0E-8 (1.00000012)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
Unit CellA= B= C: 278.144 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.173 A
CCP4 map header info
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-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-11.30636.752-0.000
Annotation DetailsMap of the proteasome subunit Rpn1 from S. cerevisiae
Supplement
Images
Images
Sample
NameRpn1
Number of Components1
Theoretical Mass0.109492MDa
Component #1: protein - Rpn1
Scientific nameRpn1
Theoretical Mass0.109492 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Staining2% uranyl acetate
Specimen Conc0.1 mg/ml
Specimen Support DetailsCarbon film on quantifoil
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose100 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000
Imaging ModeBRIGHT FIELD
Defocus800 nm - 900 nm
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Image Acquisition
Number of Digital Images71
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareImagic
Resolution By Author25 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body. Separate fitting of domains from the Rpn2 homologue
SoftwareUro
Refinement Protocolrigid body
Refinement SpaceRECIPROCAL
PDB Entry ID4SDY
Download
Data from EMDB
Header (meta data in XML format)emd-2026.xml (6.6 KB)
Map dataemd_2026.map.gz (1.2 MB)
Imagesemd-2026.png (115.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2026
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.9 KB