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- PDB-2byu: Negative stain EM reconstruction of M.tuberculosis Acr1(Hsp 16.3)... -

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Entry
Database: PDB / ID: 2byu
TitleNegative stain EM reconstruction of M.tuberculosis Acr1(Hsp 16.3) fitted with wheat sHSP dimer
ComponentsHEAT SHOCK PROTEIN 16.9BHeat shock response
KeywordsCHAPERONE / SMALL HEAT SHOCK PROTEIN / ALPHA-CRYSTALLIN
Function / homology
Function and homology information


response to salt stress / response to hydrogen peroxide / protein homooligomerization / protein self-association / unfolded protein binding / protein complex oligomerization / protein folding / response to heat / cytoplasm
Similarity search - Function
: / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
16.9 kDa class I heat shock protein 2
Similarity search - Component
Biological speciesTRITICUM AESTIVUM (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.5 Å
AuthorsKennaway, C.K. / Benesch, J.L.P. / Gohlke, U. / Wang, L. / Robinson, C.V. / Orlova, E.V. / Saibil, H.R. / Keep, N.H.
CitationJournal: J Biol Chem / Year: 2005
Title: Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis.
Authors: Christopher K Kennaway / Justin L P Benesch / Ulrich Gohlke / Luchun Wang / Carol V Robinson / Elena V Orlova / Helen R Saibil / Nicholas H Keep /
Abstract: Small heat shock proteins are a ubiquitous and diverse family of stress proteins that have in common an alpha-crystallin domain. Mycobacterium tuberculosis has two small heat shock proteins, Acr1 ...Small heat shock proteins are a ubiquitous and diverse family of stress proteins that have in common an alpha-crystallin domain. Mycobacterium tuberculosis has two small heat shock proteins, Acr1 (alpha-crystallin-related protein 1, or Hsp16.3/16-kDa antigen) and Acr2 (HrpA), both of which are highly expressed under different stress conditions. Small heat shock proteins form large oligomeric assemblies and are commonly polydisperse. Nanoelectrospray mass spectrometry showed that Acr2 formed a range of oligomers composed of dimers and tetramers, whereas Acr1 was a dodecamer. Electron microscopy of Acr2 showed a variety of particle sizes. Using three-dimensional analysis of negative stain electron microscope images, we have shown that Acr1 forms a tetrahedral assembly with 12 polypeptide chains. The atomic structure of a related alpha-crystallin domain dimer was docked into the density to build a molecular structure of the dodecameric Acr1 complex. Along with the differential regulation of these two proteins, the differences in their quaternary structures demonstrated here supports their distinct functional roles.
History
DepositionAug 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Other / Structure summary / Version format compliance
Revision 1.2Aug 30, 2017Group: Experimental preparation / Refinement description / Category: em_3d_fitting / em_sample_support
Item: _em_3d_fitting.target_criteria / _em_sample_support.grid_material / _em_sample_support.grid_mesh_size
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 16.9B
B: HEAT SHOCK PROTEIN 16.9B
C: HEAT SHOCK PROTEIN 16.9B
D: HEAT SHOCK PROTEIN 16.9B
E: HEAT SHOCK PROTEIN 16.9B
F: HEAT SHOCK PROTEIN 16.9B
G: HEAT SHOCK PROTEIN 16.9B
H: HEAT SHOCK PROTEIN 16.9B
I: HEAT SHOCK PROTEIN 16.9B
J: HEAT SHOCK PROTEIN 16.9B
K: HEAT SHOCK PROTEIN 16.9B
L: HEAT SHOCK PROTEIN 16.9B


Theoretical massNumber of molelcules
Total (without water)148,51412
Polymers148,51412
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
HEAT SHOCK PROTEIN 16.9B / Heat shock response


Mass: 12376.149 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: THE PROTEIN MODEL WAS OBTAINED FROM PDB ENTRY 1GME / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: Q41560
Sequence detailsCOOORDINATES DERIVED FROM WHEAT SHSP PDB 1GME THEREFORE PDB SEQUENCE IS NOT THAT OF THE PROTEIN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HSP 16.3 / Type: COMPLEX
Buffer solutionName: 20MM TRIS / pH: 7 / Details: 20MM TRIS
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON COATED 400 MESH COPPER GRID / Grid material: COPPER / Grid mesh size: 400 divisions/in.

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Mar 28, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 600 nm / Nominal defocus min: 390 nm / Cs: 2 mm
Specimen holderTemperature: 293 K
Image recordingElectron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 18
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 16.5 Å / Num. of particles: 6123 / Nominal pixel size: 3.33 Å / Actual pixel size: 3.33 Å
Details: DIMER ALPHA CRYSTALLIN DOMAIN OF 1GME (43-137 AND 146-151) FITTED INTO DENSITY USING URO. RESOLUTION WAS DETERMINED BY 0.5 FOURIER SHELL CORRELATION.
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient
Details: METHOD--QUALITY OF THE FIT R-FACTOR= 0.516, CROSS- CORRELATION COEFFICIENT 81.5%
Atomic model buildingPDB-ID: 1GME
RefinementHighest resolution: 16.5 Å
Refinement stepCycle: LAST / Highest resolution: 16.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9648 0 0 0 9648

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