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- EMDB-9509: Cryo-EM map of the RP region (Class1) of human 26S proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-9509
TitleCryo-EM map of the RP region (Class1) of human 26S proteasome
Map dataRP_Class1
Sample
  • Complex: human 26S proteasome
Function / homology
Function and homology information


negative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) ...negative regulation of ERAD pathway / regulation of chemotaxis / protein K48-linked deubiquitination / deubiquitinase activity / positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / proteasome accessory complex / purine ribonucleoside triphosphate binding / integrator complex / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / CD8-positive, alpha-beta T cell differentiation / CD8-positive, alpha-beta T cell homeostasis / transcription factor binding / thymic T cell selection / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / mitochondrion transport along microtubule / proteasome regulatory particle, base subcomplex / positive regulation of protein monoubiquitination / negative regulation of programmed cell death / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / protein K63-linked deubiquitination / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / cellular response to type I interferon / T-helper 17 cell differentiation / endopeptidase inhibitor activity / Cross-presentation of soluble exogenous antigens (endosomes) / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Somitogenesis / K63-linked deubiquitinase activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / flagellated sperm motility / Resolution of D-loop Structures through Holliday Junction Intermediates / sperm end piece / proteasome binding / Impaired BRCA2 binding to RAD51 / myofibril / ciliary tip / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasomal ubiquitin-independent protein catabolic process / general transcription initiation factor binding / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process / protein deubiquitination / polyubiquitin modification-dependent protein binding / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / mRNA export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / presynaptic cytosol / immune system process / regulation of G1/S transition of mitotic cell cycle / stem cell differentiation / regulation of macroautophagy / proteasome complex / enzyme regulator activity / positive regulation of interleukin-2 production / ERAD pathway / response to type II interferon / neuron projection morphogenesis / inclusion body / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / regulation of mitochondrial membrane potential / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / : / Ubiquitin interaction motif / Ubiquitin specific protease (USP) domain signature 2. / : / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / PSMD3-like, N-terminal TPR repeats / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal ...Ubiquitin carboxyl-terminal hydrolase 14-like / : / Ubiquitin interaction motif / Ubiquitin specific protease (USP) domain signature 2. / : / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / PSMD3-like, N-terminal TPR repeats / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1/SEM1 / Proteasome/cyclosome repeat / DSS1/SEM1 family / DSS1_SEM1 / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / Ubiquitin-interacting motif. / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / von Willebrand factor type A domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / : / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / HEAT repeats / PCI/PINT associated module / Proteasome subunit alpha 1 / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / : / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / VWFA domain profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / JAB/MPN domain
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 ...26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Polyubiquitin-B / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / 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 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 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 complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 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 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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

emd_9509.png

Downloads & links

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Map

FileDownload / File: emd_9509.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRP_Class1
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.06551362 - 0.15121931
Average (Standard dev.)0.00078133575 (±0.00887961)
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-0.0660.1510.001

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Supplemental data

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Sample components

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Entire : human 26S proteasome

EntireName: human 26S proteasome
Components
  • Complex: human 26S proteasome

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Supramolecule #1: human 26S proteasome

SupramoleculeName: human 26S proteasome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.5 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMTris-HClTris-HCl
150.0 mMNaClsodium chloride
5.0 mMDTTDTT
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2s before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 4881 / Average exposure time: 1.6 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 331338
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 331338
Initial angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: COMMON LINE / Software - Name: RELION (ver. 1.4)

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