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- EMDB-2036: Three-dimensional structure of Tripeptidyl peptidase II from Homo... -

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Basic information

Entry
Database: EMDB / ID: EMD-2036
TitleThree-dimensional structure of Tripeptidyl peptidase II from Homo sapiens - a spindle-shaped homo-36mer
Map dataTripeptidyl peptidase II complex of Homo sapiens
Sample
  • Sample: Tripeptidyl peptidase II of Homo Sapiens
  • Protein or peptide: Tripeptidyl peptidase II
Function / homologyPeptidase S8/S53 domain
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsSchoenegge AM / Villa E / Foerster F / Hegerl R / Peters J / Baumeister W / Rockel B
CitationJournal: Structure / Year: 2012
Title: The structure of human tripeptidyl peptidase II as determined by a hybrid approach.
Authors: Anne-Marie Schönegge / Elizabeth Villa / Friedrich Förster / Reiner Hegerl / Jürgen Peters / Wolfgang Baumeister / Beate Rockel /
Abstract: Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the ...Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation.
History
DepositionJan 20, 2012-
Header (metadata) releaseFeb 3, 2012-
Map releaseApr 13, 2012-
UpdateApr 13, 2012-
Current statusApr 13, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD_2036.png

Downloads & links

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Map

FileDownload / File: emd_2036.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTripeptidyl peptidase II complex of Homo sapiens
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.78 Å/pix.
x 384 pix.
= 683.52 Å		1.78 Å/pix.
x 384 pix.
= 683.52 Å		1.78 Å/pix.
x 384 pix.
= 683.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.03437903 - 0.0512307
Average (Standard dev.)0.00017267 (±0.00324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 683.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z683.520683.520683.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0340.0510.000

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Supplemental data

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Sample components

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Entire : Tripeptidyl peptidase II of Homo Sapiens

EntireName: Tripeptidyl peptidase II of Homo Sapiens
Components
  • Sample: Tripeptidyl peptidase II of Homo Sapiens
  • Protein or peptide: Tripeptidyl peptidase II

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Supramolecule #1000: Tripeptidyl peptidase II of Homo Sapiens

SupramoleculeName: Tripeptidyl peptidase II of Homo Sapiens / type: sample / ID: 1000 / Oligomeric state: 36-mer / Number unique components: 1
Molecular weightTheoretical: 5 MDa

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Macromolecule #1: Tripeptidyl peptidase II

MacromoleculeName: Tripeptidyl peptidase II / type: protein_or_peptide / ID: 1 / Name.synonym: Tripeptidyl peptidase II of Homo Sapiens / Number of copies: 1 / Oligomeric state: 36-mer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 5 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET30b
SequenceInterPro: Peptidase S8/S53 domain

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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

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 80 mM KPO4, 1 mM DTT, 5% glycerol
GridDetails: glow-discharged C-flat 4/1 grids covered with a thin carbon film
VitrificationCryogen name: ETHANE / Instrument: OTHER
Method: Sample was applied on grid, blotted briefly and washed twice with buffer (40 mM ammonium sulfate, pH 7.5)

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 84270 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder: side-entry cryoholder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected manually
CTF correctionDetails: each image
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: XMIPP / Details: Final map was b-factor corrected. / Number images used: 96116

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