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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
Samplehuman immunoproteasome with a novel noncompetitive inhibitor that selectively inhibits activated lymphocytes
SourceHomo sapiens / human
Map datahuman immunoproteasome with a novel noncompetitive inhibitor
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsLi H / Santos R
CitationNat Commun, 2017, 8, 1692-1692

Nat Commun, 2017, 8, 1692-1692 Yorodumi Papers
Structure of human immunoproteasome with a reversible and noncompetitive inhibitor that selectively inhibits activated lymphocytes.
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
3D viewer


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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
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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 package.

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-1 / 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-2 / 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-3 / 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-4 / 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

Specimen stateparticle
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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  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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