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- EMDB-1188: An archaeal peptidase assembles into two different quaternary str... -

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Basic information

Entry
Database: EMDB / ID: EMD-1188
TitleAn archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
Map data3D volume of the tetrahedral aminopeptidase TET1 from Pyrococus horikoshii
Sample
  • Sample: TET1 metallopeptidase from Pyrococcus horikoshii
  • Protein or peptide: cobalt activated metallopeptidase TET1
Biological speciesPyrococcus horikoshii (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.0 Å
AuthorsSchoehn G / Vellieux FM / Asuncion Dura M / Receveur-Brechot V / Fabry CM / Ruigrok RW / Ebel C / Roussel A / Franzetti B
CitationJournal: J Biol Chem / Year: 2006
Title: An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
Authors: Guy Schoehn / Frédéric M D Vellieux / M Asunción Durá / Véronique Receveur-Bréchot / Céline M S Fabry / Rob W H Ruigrok / Christine Ebel / Alain Roussel / Bruno Franzetti /
Abstract: Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea ...Cellular proteolysis involves large oligomeric peptidases that play key roles in the regulation of many cellular processes. The cobalt-activated peptidase TET1 from the hyperthermophilic Archaea Pyrococcus horikoshii (PhTET1) was found to assemble as a 12-subunit tetrahedron and as a 24-subunit octahedral particle. Both quaternary structures were solved by combining x-ray crystallography and cryoelectron microscopy data. The internal organization of the PhTET1 particles reveals highly self-compartmentalized systems made of networks of access channels extended by vast catalytic chambers. The two edifices display aminopeptidase activity, and their organizations indicate substrate navigation mechanisms different from those described in other large peptidase complexes. Compared with the tetrahedron, the octahedron forms a more expanded hollow structure, representing a new type of giant peptidase complex. PhTET1 assembles into two different quaternary structures because of quasi-equivalent contacts that previously have only been identified in viral capsids.
History
DepositionFeb 9, 2006-
Header (metadata) releaseFeb 9, 2006-
Map releaseSep 21, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.07009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1188.gif

Downloads & links

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Map

FileDownload / File: emd_1188.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D volume of the tetrahedral aminopeptidase TET1 from Pyrococus horikoshii
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 0.0251 / Movie #1: 0.07009
Minimum - Maximum-0.118029 - 0.16105
Average (Standard dev.)0.000749406 (±0.0121943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1180.1610.001

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Supplemental data

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Sample components

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Entire : TET1 metallopeptidase from Pyrococcus horikoshii

EntireName: TET1 metallopeptidase from Pyrococcus horikoshii
Components
  • Sample: TET1 metallopeptidase from Pyrococcus horikoshii
  • Protein or peptide: cobalt activated metallopeptidase TET1

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Supramolecule #1000: TET1 metallopeptidase from Pyrococcus horikoshii

SupramoleculeName: TET1 metallopeptidase from Pyrococcus horikoshii / type: sample / ID: 1000 / Oligomeric state: 12 mer / Number unique components: 1
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa / Method: Analytical ultracentrifugation

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Macromolecule #1: cobalt activated metallopeptidase TET1

MacromoleculeName: cobalt activated metallopeptidase TET1 / type: protein_or_peptide / ID: 1 / Details: Pyrococcus horikoshii / Number of copies: 12 / Oligomeric state: 12-mer / Recombinant expression: Yes
Source (natural)Organism: Pyrococcus horikoshii (archaea) / synonym: PH0519 / Tissue: Pyrococcus horikoshii / Cell: Pyrococcus horikoshii / Organelle: Pyrococcus horikoshii
Recombinant expressionOrganism: Pyrococcus horikoshii (archaea)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE
Details: Quantifoil R2 1 grids (Quantifoil Micro Tools GmbH, Germany) were loaded with 4 ul of sample at 1 mg ml, blotted and rapidly frozen in liquid ethane within a liquid nitrogen bath using a Zeiss cryoplunger
GridDetails: Quantifoil R2/1 grids
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Zeiss cryoplunger

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 100 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: bjective lens astigmatism was corrected at
DateJan 1, 2002
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 15 / Average electron dose: 15 e/Å2 / Od range: 1.2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: ctfmix
Final two d classificationNumber classes: 159
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: spider / Details: 8000 particles in 159 class average / Number images used: 8000

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Atomic model buiding 1

DetailsProtocol: Rigid Body. colores from Situs
RefinementProtocol: RIGID BODY FIT

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