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- EMDB-1823: Clostridium thermocellum Mini-Cellulosome -

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Basic information

Entry
Database: EMDB / ID: EMD-1823
TitleClostridium thermocellum Mini-Cellulosome
Map dataThis is an image of a surface rendered side-view of Clostridium thermocellum Mini-Cellulosome
Sample
  • Sample: Mini-Cellulosome of Clostridium thermocillium
  • Protein or peptide: Cohesin domains
  • Protein or peptide: Clostridium thermocellum Cel8A
KeywordsCellulosome / CipA / Cohesin / Dockerin
Biological speciesClostridium thermocellum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 35.0 Å
AuthorsGarcia-Alvarez B / Melero R / Dias FMV / Prates JAM / Fontes CMGA / Smith SP / Joao Romao M / Carvalho AL / Llorca O
CitationJournal: J Mol Biol / Year: 2011
Title: Molecular architecture and structural transitions of a Clostridium thermocellum mini-cellulosome.
Authors: Begoña García-Alvarez / Roberto Melero / Fernando M V Dias / José A M Prates / Carlos M G A Fontes / Steven P Smith / Maria João Romão / Ana Luísa Carvalho / Oscar Llorca /
Abstract: The cellulosome is a highly elaborate cell-bound multienzyme complex that efficiently orchestrates the deconstruction of cellulose and hemicellulose, two of the nature's most abundant polymers. ...The cellulosome is a highly elaborate cell-bound multienzyme complex that efficiently orchestrates the deconstruction of cellulose and hemicellulose, two of the nature's most abundant polymers. Understanding the intricacy of these nanomachines evolved by anaerobic microbes could sustain the development of an effective process for the conversion of lignocellulosic biomass to bio-ethanol. In Clostridium thermocellum, cellulosome assembly is mediated by high-affinity protein:protein interactions (>10(9) M(-1)) between dockerin modules found in the catalytic subunits and cohesin modules located in a non-catalytic protein scaffold termed CipA. Whereas the atomic structures of several cellulosomal components have been elucidated, the structural organization of the complete cellulosome remains elusive. Here, we reveal that a large fragment of the cellulosome presents a mostly compact conformation in solution, by solving the three-dimensional structure of a C. thermocellum mini-cellulosome comprising three consecutive cohesin modules, each bound to one Cel8A cellulase, at 35 Å resolution by cryo-electron microscopy. Interestingly, the three cellulosomal catalytic domains are found alternately projected outward from the CipA scaffold in opposite directions, in an arrangement that could expand the area of the substrate accessible to the catalytic domains. In addition, the cellulosome can transit from this compact conformation to a multitude of diverse and flexible structures, where the linkers between cohesin modules are extended and flexible. Thus, structural transitions controlled by changes in the degree of flexibility of linkers connecting consecutive cohesin modules could regulate the efficiency of substrate recognition and hydrolysis.
History
DepositionNov 18, 2010-
Header (metadata) releaseNov 26, 2010-
Map releaseFeb 15, 2011-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1823.jpg

Downloads & links

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Map

FileDownload / File: emd_1823.map.gz / Format: CCP4 / Size: 4.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is an image of a surface rendered side-view of Clostridium thermocellum Mini-Cellulosome
Voxel sizeX=Y=Z: 4.2 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-5.57591 - 26.2301
Average (Standard dev.)-0.00035825 (±0.754278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions104104104
Spacing104104104
CellA=B=C: 436.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z104104104
origin x/y/z0.0000.0000.000
length x/y/z436.800436.800436.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS104104104
D min/max/mean-5.57626.230-0.000

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Supplemental data

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Sample components

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Entire : Mini-Cellulosome of Clostridium thermocillium

EntireName: Mini-Cellulosome of Clostridium thermocillium
Components
  • Sample: Mini-Cellulosome of Clostridium thermocillium
  • Protein or peptide: Cohesin domains
  • Protein or peptide: Clostridium thermocellum Cel8A

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Supramolecule #1000: Mini-Cellulosome of Clostridium thermocillium

SupramoleculeName: Mini-Cellulosome of Clostridium thermocillium / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 200 KDa

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Macromolecule #1: Cohesin domains

MacromoleculeName: Cohesin domains / type: protein_or_peptide / ID: 1 / Name.synonym: C3-C4-C5 cohesin domains of CipA / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Clostridium thermocellum (bacteria)
Molecular weightTheoretical: 52.1 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET3a (Novagen)

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Macromolecule #2: Clostridium thermocellum Cel8A

MacromoleculeName: Clostridium thermocellum Cel8A / type: protein_or_peptide / ID: 2
Name.synonym: N-terminal glycoside hydrolase family 8 (GH8) catalytic domain
Number of copies: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Clostridium thermocellum (bacteria)
Molecular weightTheoretical: 49.9 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET3a (Novagen)

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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

BufferpH: 7.5
Details: 50 mM Hepes/HCl buffer, pH 7.5, containing 200 mM NaCl and 2 mM CaCl2
GridDetails: QUANTIFOIL R 1.2/1.3
VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 50000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
DateJun 25, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Details: 0.42 nm per pixel, final sampling / Bits/pixel: 16

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Image processing

CTF correctionDetails: Each CCD Frame
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5612

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Atomic model buiding 1

Initial modelPDB ID:

2ccl

SoftwareName: Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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Atomic model buiding 2

Initial modelPDB ID:

1cem

SoftwareName: Chimera
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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