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- PDB-5nms: Hsp21 dodecamer, structural model based on cryo-EM and homology m... -

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Basic information

Entry
Database: PDB / ID: 5nms
TitleHsp21 dodecamer, structural model based on cryo-EM and homology modelling
Descriptor25.3 kDa heat shock protein, chloroplastic
KeywordsCHAPERONE / stress response / heat shock protein / chaperone / all-beta greek key
Specimen sourceArabidopsis thaliana / plant / thale cress / Mouse-ear cress / シロイヌナズナ /
MethodElectron microscopy (10 Å resolution / Particle / Single particle)
AuthorsRutsdottir, G. / Harmark, J. / Koeck, P.J.B. / Hebert, H. / Soderberg, C.A.G. / Emanuelsson, C.
CitationJ. Biol. Chem., 2017, 292, 8103-8121

J. Biol. Chem., 2017, 292, 8103-8121 StrPapers
Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity.
Gudrun Rutsdottir / Johan Härmark / Yoran Weide / Hans Hebert / Morten I Rasmussen / Sven Wernersson / Michal Respondek / Mikael Akke / Peter Højrup / Philip J B Koeck / Christopher A G Söderberg / Cecilia Emanuelsson

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 7, 2017 / Release: May 3, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1May 24, 2017Structure modelDatabase references
1.2Aug 30, 2017Structure modelData collectionem_image_scans / em_software_em_software.name
1.3Sep 13, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: 25.3 kDa heat shock protein, chloroplastic
B: 25.3 kDa heat shock protein, chloroplastic
C: 25.3 kDa heat shock protein, chloroplastic
E: 25.3 kDa heat shock protein, chloroplastic
D: 25.3 kDa heat shock protein, chloroplastic
F: 25.3 kDa heat shock protein, chloroplastic
G: 25.3 kDa heat shock protein, chloroplastic
H: 25.3 kDa heat shock protein, chloroplastic
I: 25.3 kDa heat shock protein, chloroplastic
K: 25.3 kDa heat shock protein, chloroplastic
J: 25.3 kDa heat shock protein, chloroplastic
L: 25.3 kDa heat shock protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)169,02712
Polyers169,02712
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)22350
ΔGint (kcal/M)-71
Surface area (Å2)93570
MethodPISA

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Components

#1: Polypeptide(L)
25.3 kDa heat shock protein, chloroplastic / AtHsp25.3


Mass: 16393.787 Da / Num. of mol.: 6
Source: (gene. exp.) Arabidopsis thaliana / plant / thale cress / シロイヌナズナ /
References: UniProt: P31170

Cellular component

Biological process

#2: Polypeptide(L)
25.3 kDa heat shock protein, chloroplastic / AtHsp25.3


Mass: 11777.428 Da / Num. of mol.: 6
Source: (gene. exp.) Arabidopsis thaliana / plant / thale cress / シロイヌナズナ /
References: UniProt: P31170

Cellular component

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Hsp21 dodecamer, a chloroplast small heat shock protein chaperone
Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 2100F
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.4 e/Å2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2PARTICLE SELECTION1
2EMAN2IMAGE ACQUISITION1
4EMAN2CTF CORRECTION1
7UCSF Chimera11MODEL FITTING1
9EMAN2INITIAL EULER ASSIGNMENT1
10RELION3FINAL EULER ASSIGNMENT1
12RELION3RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNumber of particles selected: 33456
SymmetryPoint symmetry: D3
3D reconstructionResolution: 1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 18407 / Symmetry type: POINT

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