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- PDB-7bzy: Hsp21-DXPS -

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Basic information

Entry
Database: PDB / ID: 7bzy
TitleHsp21-DXPS
Components
  • 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
  • Heat shock protein 21, chloroplasticHeat shock response
KeywordsTRANSFERASE/CHAPERONE / Hsp21-DXPS / PLANT PROTEIN / TRANSFERASE / CHAPERONE / TRANSFERASE-CHAPERONE complex
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / transketolase or transaldolase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / chloroplast nucleoid / chloroplast organization / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process ...1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / transketolase or transaldolase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / chloroplast nucleoid / chloroplast organization / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / protein folding chaperone complex / chloroplast stroma / response to light stimulus / chloroplast / : / response to heat / regulation of DNA-templated transcription / identical protein binding / metal ion binding
Similarity search - Function
Heat shock protein 21-like / Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase binding site / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain ...Heat shock protein 21-like / Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase binding site / Transketolase signature 1. / Transketolase signature 2. / Transketolase, N-terminal / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / Transketolase, C-terminal domain / Transketolase, C-terminal domain / HSP20-like chaperone / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Heat shock protein 21, chloroplastic / 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLau, W.C.Y.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14105517 Hong Kong
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of substrate recognition and thermal protection by a small heat shock protein.
Authors: Chuanyang Yu / Stephen King Pong Leung / Wenxin Zhang / Louis Tung Faat Lai / Ying Ki Chan / Man Chit Wong / Samir Benlekbir / Yong Cui / Liwen Jiang / Wilson Chun Yu Lau /
Abstract: Small heat shock proteins (sHsps) bind unfolding proteins, thereby playing a pivotal role in the maintenance of proteostasis in virtually all living organisms. Structural elucidation of sHsp- ...Small heat shock proteins (sHsps) bind unfolding proteins, thereby playing a pivotal role in the maintenance of proteostasis in virtually all living organisms. Structural elucidation of sHsp-substrate complexes has been hampered by the transient and heterogeneous nature of their interactions, and the precise mechanisms underlying substrate recognition, promiscuity, and chaperone activity of sHsps remain unclear. Here we show the formation of a stable complex between Arabidopsis thaliana plastid sHsp, Hsp21, and its natural substrate 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) under heat stress, and report cryo-electron microscopy structures of Hsp21, DXPS and Hsp21-DXPS complex at near-atomic resolution. Monomeric Hsp21 binds across the dimer interface of DXPS and engages in multivalent interactions by recognizing highly dynamic structural elements in DXPS. Hsp21 partly unfolds its central α-crystallin domain to facilitate binding of DXPS, which preserves a native-like structure. This mode of interaction suggests a mechanism of sHsps anti-aggregation activity towards a broad range of substrates.
History
DepositionApr 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
11: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
12: Heat shock protein 21, chloroplastic
13: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)172,5823
Polymers172,5823
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic / / DXPS / Protein CLOROPLASTOS ALTERADOS 1


Mass: 74463.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DXS, CLA1, DEF, At4g15560, dl3821w / Production host: Escherichia coli (E. coli)
References: UniProt: Q38854, 1-deoxy-D-xylulose-5-phosphate synthase
#2: Protein Heat shock protein 21, chloroplastic / Heat shock response / 25.3 kDa heat shock protein / chloroplastic / AtHsp25.3


Mass: 23654.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HSP21, HSP25.3, At4g27670, T29A15.160 / Production host: Escherichia coli (E. coli) / References: UniProt: P31170

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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: DXPS,Hsp21 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162426 / Symmetry type: POINT

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