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- EMDB-7010: Cryo-EM structure of human immunoproteasome with a novel noncompe... -

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Basic information

Entry
Database: EMDB / ID: 7010
TitleCryo-EM structure of human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Map datahuman immunoproteasome with a novel noncompetitive inhibitor
Samplehuman immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
  • (Proteasome subunit beta type- ...) x 7
  • (Proteasome subunit alpha type- ...) x 7
  • ligand
Function / homologyProteasome beta subunits C terminal / Proteasome subunit beta type 10 / Proteasome subunit alpha 3 / Proteasome subunit beta type 8 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 ...Proteasome beta subunits C terminal / Proteasome subunit beta type 10 / Proteasome subunit alpha 3 / Proteasome subunit beta type 8 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit beta type 9 / Proteasome subunit A N-terminal signature / Proteasome subunit alpha5 / Proteasome beta 3 subunit / Nucleophile aminohydrolases, N-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Proteasome, subunit alpha/beta / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit / Proteasome alpha-type subunits signature. / Asymmetric localization of PCP proteins / Vpu mediated degradation of CD4 / ABC-family proteins mediated transport / Regulation of ornithine decarboxylase (ODC) / Autodegradation of the E3 ubiquitin ligase COP1 / FCERI mediated NF-kB activation / Separation of Sister Chromatids / Regulation of activated PAK-2p34 by proteasome mediated degradation / Downstream TCR signaling / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / Vif-mediated degradation of APOBEC3G / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Proteasome beta-type subunits signature. / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / Cross-presentation of soluble exogenous antigens (endosomes) / ER-Phagosome pathway / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Activation of NF-kappaB in B cells / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Peptidase T1A, proteasome beta-subunit / AUF1 (hnRNP D0) binds and destabilizes mRNA / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neutrophil degranulation / Regulation of PTEN stability and activity / Regulation of RUNX3 expression and activity / Regulation of RUNX2 expression and activity / UCH proteinases / Degradation of AXIN / Ub-specific processing proteases / CDT1 association with the CDC6:ORC:origin complex / MAPK6/MAPK4 signaling / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Neddylation / Defective CFTR causes cystic fibrosis / The role of GTSE1 in G2/M progression after G2 checkpoint / Interferon alpha/beta signaling / Degradation of DVL / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Antigen processing: Ubiquitination & Proteasome degradation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / regulation of cysteine-type endopeptidase activity / spermatoproteasome complex / purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / immune system process / proteasome core complex / fat cell differentiation / myofibril / humoral immune response / antigen processing and presentation / NF-kappaB binding / proteasome complex / sarcomere
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsLi H / Santos R
CitationJournal: Nat Commun / Year: 2017
Title: Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
Authors: Ruda de Luna Almeida Santos / Lin Bai / Pradeep K Singh / Naoka Murakami / Hao Fan / Wenhu Zhan / Yingrong Zhu / Xiuju Jiang / Kaiming Zhang / Jean Pierre Assker / Carl F Nathan / Huilin Li / Jamil Azzi / Gang Lin
Validation ReportPDB-ID: 6avo

SummaryFull reportAbout validation report
DateDeposition: Sep 4, 2017 / Header (metadata) release: Sep 27, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0383
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0383
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6avo
  • Surface level: 0.0383
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7010.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.2 Å/pix.
= 307.2 Å
256 pix
1.2 Å/pix.
= 307.2 Å
256 pix
1.2 Å/pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour Level:0.0383 (by author), 0.0383 (movie #1):
Minimum - Maximum-0.15268016 - 0.26070794
Average (Standard dev.)0.00067930506 (0.0088249175)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z307.200307.200307.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1530.2610.001

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Supplemental data

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Sample components

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Entire human immunoproteasome with a novel noncompetitive inhibitor that...

EntireName: human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Number of components: 16

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Component #1: protein, human immunoproteasome with a novel noncompetitive inhib...

ProteinName: human immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Proteasome subunit beta type-9

ProteinName: Proteasome subunit beta type-9 / Recombinant expression: No
MassTheoretical: 21.295 kDa
SourceSpecies: Homo sapiens (human)

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Component #3: protein, Proteasome subunit beta type-10

ProteinName: Proteasome subunit beta type-10 / Recombinant expression: No
MassTheoretical: 24.674248 kDa
SourceSpecies: Homo sapiens (human)

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Component #4: protein, Proteasome subunit beta type-8

ProteinName: Proteasome subunit beta type-8 / Recombinant expression: No
MassTheoretical: 22.685633 kDa
SourceSpecies: Homo sapiens (human)

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Component #5: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Recombinant expression: No
MassTheoretical: 29.595627 kDa
SourceSpecies: Homo sapiens (human)

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Component #6: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Recombinant expression: No
MassTheoretical: 26.435977 kDa
SourceSpecies: Homo sapiens (human)

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Component #7: protein, Proteasome subunit alpha type-7

ProteinName: Proteasome subunit alpha type-7 / Recombinant expression: No
MassTheoretical: 27.929891 kDa
SourceSpecies: Homo sapiens (human)

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Component #8: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Recombinant expression: No
MassTheoretical: 28.469252 kDa
SourceSpecies: Homo sapiens (human)

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Component #9: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Recombinant expression: No
MassTheoretical: 27.432459 kDa
SourceSpecies: Homo sapiens (human)

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Component #10: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Recombinant expression: No
MassTheoretical: 29.525842 kDa
SourceSpecies: Homo sapiens (human)

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Component #11: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Recombinant expression: No
MassTheoretical: 25.927535 kDa
SourceSpecies: Homo sapiens (human)

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Component #12: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Recombinant expression: No
MassTheoretical: 23.578986 kDa
SourceSpecies: Homo sapiens (human)

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Component #13: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Recombinant expression: No
MassTheoretical: 22.864277 kDa
SourceSpecies: Homo sapiens (human)

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Component #14: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Recombinant expression: No
MassTheoretical: 22.972896 kDa
SourceSpecies: Homo sapiens (human)

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Component #15: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Recombinant expression: No
MassTheoretical: 24.41474 kDa
SourceSpecies: Homo sapiens (human)

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Component #16: ligand, N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-te...

LigandName: N~1~-{2-[([1,1'-biphenyl]-3-carbonyl)amino]ethyl}-N~4~-tert-butyl-N~2~-(3-phenylpropanoyl)-L-aspartamide
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.542669 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 75017
3D reconstructionSoftware: RELION / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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