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- EMDB-4120: In situ TPPII 32mer -

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Basic information

Entry
Database: EMDB / ID: 4120
TitleIn situ TPPII 32mer
SampleTripeptidyl peptidase II
SourceRattus / mammal / image: Rattus norvegicus
Map datain situ TPPII 32mer
Methodsubtomogram averaging, at 36.5 Å resolution
AuthorsFukuda Y / Beck F / Baumeister W
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 4412-4417

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 4412-4417 StrPapers
In situ structural studies of tripeptidyl peptidase II (TPPII) reveal spatial association with proteasomes.
Yoshiyuki Fukuda / Florian Beck / Jürgen M Plitzko / Wolfgang Baumeister

DateDeposition: Sep 28, 2016 / Header (metadata) release: Nov 9, 2016 / Map release: Apr 12, 2017 / Last update: Sep 28, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.8
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 2.8
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_4120.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
4.21 Å/pix.
= 842. Å
200 pix
4.21 Å/pix.
= 842. Å
200 pix
4.21 Å/pix.
= 842. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.21 Å
Density
Contour Level:2.8 (by author), 2.8 (movie #1):
Minimum - Maximum-0.6999472 - 0.8225197
Average (Standard dev.)-0.0007039142 (0.09365163)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 842 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z4.214.214.21
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z842.000842.000842.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-7.5728.883-0.001

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Supplemental data

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Sample components

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Entire Tripeptidyl peptidase II

EntireName: Tripeptidyl peptidase II / Details: 32mer / Number of components: 1
MassTheoretical: 4.4 MDa

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Component #1: protein, Tripeptidyl peptidase II

ProteinName: Tripeptidyl peptidase II / Details: 32mer / Recombinant expression: No
MassTheoretical: 4.4 MDa
SourceSpecies: Rattus / mammal / image: Rattus norvegicus
Source (natural)Organ or tissue: hippocampus

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 310 K / Humidity: 90 %

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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: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 33000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 1000 nm / Energy filter: Gatan / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -60 - 60 deg. / Temperature: K ( 70 - 70 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: D2 (2*2 fold dihedral)
3D reconstructionSoftware: Pytom / Resolution: 36.5 Å / Resolution method: FSC 0.143 CUT-OFF

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