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Entry
Database: EMDB / ID: EMD-2981
TitleCryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core
Map datareconstruction of the human 20S proteasome core, as determined by the 3D reconstitution algorithm, without further masking, sharpening or Fourier filtering
Sample
  • Sample: human 20S proteasome core
  • Protein or peptide: x 14 types
Keywordsproteasome / 20S / human / AdaAhx3L3VS / ligand / inhibitor / drug design
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / sarcomere / proteasome complex / ciliary basal body / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Ubiquitin-dependent degradation of Cyclin D / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of inflammatory response to antigenic stimulus / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / P-body / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / : / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / CLEC7A (Dectin-1) signaling / Regulation of expression of SLITs and ROBOs / nuclear matrix / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / response to oxidative stress / nuclear body / Ub-specific processing proteases / ribosome / cadherin binding / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / mitochondrion / proteolysis / RNA binding / extracellular exosome / extracellular region
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / 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. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit alpha type-7 / 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 ...Proteasome subunit alpha type-7 / 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 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
Authorsda Fonseca PCA / Morris EP
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core.
Authors: Paula C A da Fonseca / Edward P Morris /
Abstract: The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, ...The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.
History
DepositionApr 22, 2015-
Header (metadata) releaseMay 27, 2015-
Map releaseJul 15, 2015-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5a0q
  • Surface level: 3.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5a0q
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2981.png

Downloads & links

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Map

FileDownload / File: emd_2981.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of the human 20S proteasome core, as determined by the 3D reconstitution algorithm, without further masking, sharpening or Fourier filtering
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2 / Movie #1: 3.2
Minimum - Maximum-13.471917149999999 - 16.751863480000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-129-129-129
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-129-129-129
NC/NR/NS256256256
D min/max/mean-13.47216.7520.000

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Supplemental data

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Sample components

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Entire : human 20S proteasome core

EntireName: human 20S proteasome core
Components
  • Sample: human 20S proteasome core
  • Protein or peptide: Proteasome subunit alpha type-6
  • Protein or peptide: Proteasome subunit alpha type-2
  • Protein or peptide: Proteasome subunit alpha type-4
  • Protein or peptide: Proteasome subunit alpha type-7
  • Protein or peptide: Proteasome subunit alpha type-5
  • Protein or peptide: Proteasome subunit alpha type-1
  • Protein or peptide: Proteasome subunit alpha type-3
  • Protein or peptide: Proteasome subunit beta type-6
  • Protein or peptide: Proteasome subunit beta type-7
  • Protein or peptide: Proteasome subunit beta type-3
  • Protein or peptide: Proteasome subunit beta type-2
  • Protein or peptide: Proteasome subunit beta type-5
  • Protein or peptide: Proteasome subunit beta type-1
  • Protein or peptide: Proteasome subunit beta type-4

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Supramolecule #1000: human 20S proteasome core

SupramoleculeName: human 20S proteasome core / type: sample / ID: 1000 / Details: the sample was monodisperse / Oligomeric state: 14-mer / Number unique components: 14
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 1 / Name.synonym: PSMA6, proteasome alpha1 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 27 KDa
SequenceUniProtKB: Proteasome subunit alpha type-6

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Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Name.synonym: PSMA2, proteasome alpha2 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 26 KDa
SequenceUniProtKB: Proteasome subunit alpha type-2

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Macromolecule #3: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 3 / Name.synonym: PSMA4, proteasome alpha3 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 29 KDa
SequenceUniProtKB: Proteasome subunit alpha type-4

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Macromolecule #4: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 4 / Name.synonym: PSMA7, proteasome alpha4 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 28 KDa
SequenceUniProtKB: Proteasome subunit alpha type-7

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Macromolecule #5: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 5 / Name.synonym: PSMA5, proteasome alpha5 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 26 KDa
SequenceUniProtKB: Proteasome subunit alpha type-5

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Macromolecule #6: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 6 / Name.synonym: PSMA1, proteasome alpha6 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 30 KDa
SequenceUniProtKB: Proteasome subunit alpha type-1

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Macromolecule #7: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 7 / Name.synonym: PSMA3, proteasome alpha7 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 28 KDa
SequenceUniProtKB: Proteasome subunit alpha type-3

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Macromolecule #8: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 8 / Name.synonym: PSMB6, proteasome beta1
Details: Subunit partially bound to the inhibitor adamantane-acetyl-(6-aminohexanoyl)3-(leucinyl)3-vinyl-(methyl)-sulfone (AdaAhx3L3VS)
Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 25 KDa
SequenceUniProtKB: Proteasome subunit beta type-6

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Macromolecule #9: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 9 / Name.synonym: PSMB7, proteasome beta2
Details: Subunit partially bound to the inhibitor adamantane-acetyl-(6-aminohexanoyl)3-(leucinyl)3-vinyl-(methyl)-sulfone (AdaAhx3L3VS)
Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 30 KDa
SequenceUniProtKB: Proteasome subunit beta type-7

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Macromolecule #10: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 10 / Name.synonym: PSMB3, proteasome beta3 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 23 KDa
SequenceUniProtKB: Proteasome subunit beta type-3

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Macromolecule #11: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 11 / Name.synonym: PSMB2, proteasome beta4 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 23 KDa
SequenceUniProtKB: Proteasome subunit beta type-2

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Macromolecule #12: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 12 / Name.synonym: PSMB5, proteasome beta5
Details: Subunit bound to the inhibitor adamantane-acetyl-(6-aminohexanoyl)3-(leucinyl)3-vinyl-(methyl)-sulfone (AdaAhx3L3VS)
Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 28 KDa
SequenceUniProtKB: Proteasome subunit beta type-5

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Macromolecule #13: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 13 / Name.synonym: PSMB1, proteasome beta6 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 26 KDa
SequenceUniProtKB: Proteasome subunit beta type-1

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Macromolecule #14: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 14 / Name.synonym: PSMB4, proteasome beta7 / Number of copies: 2 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: human / Cell: erythrocytes
Molecular weightTheoretical: 29 KDa
SequenceUniProtKB: Proteasome subunit beta type-4

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris-HCl, 5 mM MgCl2 and 1mM dithiotreitol
GridDetails: 1.2/1.3 Quantifoil coated with freshly floated thin layer of carbon, glow discharged in amylamine atmosphere
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: blot 2.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 85 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at the recording magnification
DetailsEach exposure was recorded as 17 individual frames captured at a rate of 0.056 second/frame, with an electron dose of 2.8 electrons/square angstrom. Data-set recorded using EPU software.
DateFeb 4, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 960 / Average electron dose: 48 e/Å2
Details: each image is the sum of 17 frames recorded by the direct electron detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 134461 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsautomatic particle picking followed by careful manual removal of false positives and addition of false negatives; high resolution analysis was done using the sum of frames 3-10
CTF correctionDetails: full recorded image
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: Spider, Tigris, Imagic
Details: the analysis was done using a data-set recorded during a single EM session
Number images used: 76500
Final angle assignmentDetails: Beta 0 degrees, gamma 90 degrees (IMAGIC)

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Atomic model buiding 1

Initial modelPDB ID:

3une


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S / Chain - #19 - Chain ID: T / Chain - #20 - Chain ID: U / Chain - #21 - Chain ID: V / Chain - #22 - Chain ID: W / Chain - #23 - Chain ID: X / Chain - #24 - Chain ID: Y / Chain - #25 - Chain ID: Z / Chain - #26 - Chain ID: a / Chain - #27 - Chain ID: b
SoftwareName: Coot, Phenix
DetailsThe model of the human 20S proteasome core was built based on the X-ray crystal structure of the mouse constitutive apo 20S proteasome core (3UNE) using real space refinement in Coot and Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5a0q:
Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

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