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- EMDB-9510: Cryo-EM map of the RP region (Class2) of human 26S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-9510
TitleCryo-EM map of the RP region (Class2) of human 26S proteasome
Map data
Samplehuman 26S proteasomeProteasome
Function / homology
Function and homology information


negative regulation of ER-associated ubiquitin-dependent protein catabolic process / regulation of chemotaxis / purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex ...negative regulation of ER-associated ubiquitin-dependent protein catabolic process / regulation of chemotaxis / purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / regulation of endopeptidase activity / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / Lys63-specific deubiquitinase activity / mitochondrion transport along microtubule / cytosolic proteasome complex / Regulation of ornithine decarboxylase (ODC) / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / Cross-presentation of soluble exogenous antigens (endosomes) / negative regulation of programmed cell death / myofibril / male meiosis I / proteasome binding / endopeptidase inhibitor activity / female gonad development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / seminiferous tubule development / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein catabolic process / polyubiquitin modification-dependent protein binding / negative regulation of G2/M transition of mitotic cell cycle / proteasome storage granule / Wnt signaling pathway, planar cell polarity pathway / regulation of neuron death / NIK/NF-kappaB signaling / energy homeostasis / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / endopeptidase activator activity / proteasome core complex / regulation of hematopoietic stem cell differentiation / isopeptidase activity / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / regulation of mitotic cell cycle phase transition / NF-kappaB binding / proteasome core complex, alpha-subunit complex / stem cell differentiation / regulation of cellular amino acid metabolic process / proteasome assembly / threonine-type endopeptidase activity / polysome / ciliary basal body / ubiquitin-dependent ERAD pathway / sarcomere / Maturation of protein E / Maturation of protein E / Myoclonic epilepsy of Lafora / inclusion body / ER Quality Control Compartment (ERQC) / endoplasmic reticulum mannose trimming / Glycogen synthesis / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / mRNA export from nucleus / Alpha-protein kinase 1 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK1 recruits IKK complex / response to organonitrogen compound / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Negative regulation of FLT3 / TICAM1-dependent activation of IRF3/IRF7 / endoplasmic reticulum quality control compartment / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / APC/C:Cdc20 mediated degradation of Cyclin B / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Downregulation of ERBB4 signaling / Pexophagy / PINK1-PRKN Mediated Mitophagy / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Josephin domain DUBs / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 ...Ubiquitin carboxyl-terminal hydrolase 14-like / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit, C-terminal / DSS1/SEM1 / DSS1_SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1/SEM1 family / 26S proteasome subunit RPN6 C-terminal helix domain / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 14 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / RPN1, N-terminal / RPN1 N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / 26S Proteasome regulatory subunit 6B / von Willebrand factor type A domain / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / CSN8/PSMD8/EIF3K family / CSN8/PSMD8/EIF3K / 26S proteasome regulatory subunit P45-like / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Rpn11/EIF3F, C-terminal / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin carboxyl-terminal hydrolase / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin specific protease (USP) domain profile. / Ubiquitin specific protease domain / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit beta 5 / Proteasome subunit beta 7 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / von Willebrand factor (vWF) type A domain / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome beta 3 subunit / Proteasome subunit beta 2 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / AAA ATPase, AAA+ lid domain / AAA+ lid domain / JAB/MPN domain / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / von Willebrand factor, type A / Proteasome alpha-type subunit profile. / MPN domain / Proteasome alpha-type subunit / MPN domain profile. / Proteasome beta-type subunit profile. / Proteasome B-type subunit / Proteasome subunit
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B / 26S proteasome complex subunit SEM1 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / Ubiquitin carboxyl-terminal hydrolase 14 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit 8 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 ...26S proteasome regulatory subunit 6B / 26S proteasome complex subunit SEM1 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / Ubiquitin carboxyl-terminal hydrolase 14 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit 8 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 7 / Proteasome subunit beta type-1 / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-1 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsHuang XL / Luan B / Wu JP / Shi YG
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: An atomic structure of the human 26S proteasome.
Authors: Xiuliang Huang / Bai Luan / Jianping Wu / Yigong Shi /
Abstract: We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory ...We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function.
History
DepositionJul 1, 2016-
Header (metadata) releaseJul 27, 2016-
Map releaseJul 27, 2016-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.044
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9510.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å
1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.102109775 - 0.17986521
Average (Standard dev.)0.0015848584 (±0.010668034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1020.1800.002

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Supplemental data

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Sample components

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Entire human 26S proteasome

EntireName: human 26S proteasomeProteasome / Number of Components: 1

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Component #1: protein, human 26S proteasome

ProteinName: human 26S proteasomeProteasome / Recombinant expression: No
MassTheoretical: 2.5 MDa
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 281 K / Humidity: 100 % / Details: blot for 2s before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 37 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Imaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (70.0 - K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 4881

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 115306
3D reconstructionSoftware: RELION / Resolution: 4.6 Å / Resolution Method: FSC 0.143 CUT-OFF

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