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- EMDB-30263: Hsp21-DXPS -

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Basic information

Entry
Database: EMDB / ID: EMD-30263
TitleHsp21-DXPS
Map data
Sample
  • Complex: DXPS,Hsp21
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
    • Protein or peptide: Heat shock protein 21, chloroplasticHeat shock response
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLau WCY
Funding support Hong Kong, 1 items
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, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
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  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-7bzy
  • Surface level: 0.015
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30263.png

Downloads & links

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Map

FileDownload / File: emd_30263.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.015
Minimum - Maximum-0.044569228 - 0.0963245
Average (Standard dev.)-4.306246e-05 (±0.004049581)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 197.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z197.760197.760197.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0450.096-0.000

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Supplemental data

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Additional map: Sharpened and filtered map

Fileemd_30263_additional_1.map
AnnotationSharpened and filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30263_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30263_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DXPS,Hsp21

EntireName: DXPS,Hsp21
Components
  • Complex: DXPS,Hsp21
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
    • Protein or peptide: Heat shock protein 21, chloroplasticHeat shock response

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Supramolecule #1: DXPS,Hsp21

SupramoleculeName: DXPS,Hsp21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic

MacromoleculeName: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 1-deoxy-D-xylulose-5-phosphate synthase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 74.463719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADLNWISAG HAIADVGTAS LAEKGEYYSN RPPTPLLDTI NYPIHMKNLS VKELKQLSDE LRSDVIFNVS KTGGHLGSSL GVVELTVAL HYIFNTPQDK ILWDVGHQSY PHKILTGRRG KMPTMRQTNG LSGFTKRGES EHDCFGTGHS STTISAGLGM A VGRDLKGK ...String:
MADLNWISAG HAIADVGTAS LAEKGEYYSN RPPTPLLDTI NYPIHMKNLS VKELKQLSDE LRSDVIFNVS KTGGHLGSSL GVVELTVAL HYIFNTPQDK ILWDVGHQSY PHKILTGRRG KMPTMRQTNG LSGFTKRGES EHDCFGTGHS STTISAGLGM A VGRDLKGK NNNVVAVIGD GAMTAGQAYE AMNNAGYLDS DMIVILNDNK QVSLPTATLD GPSPPVGALS SALSRLQSNP AL RELREVA KGMTKQIGGP MHQLAAKVDE YARGMISGTG SSLFEELGLY YIGPVDGHNI DDLVAILKEV KSTRTTGPVL IHV VTEKGR GYPYAERADD KYHGVVKFDP ATGRQFKTTN KTQSYTTYFA EALVAEAEVD KDVVAIHAAM GGGTGLNLFQ RRFP TRCFD VGIAEQHAVT FAAGLACEGL KPFCAIYSSF MQRAYDQVVH DVDLQKLPVR FAMDRAGLVG ADGPTHCGAF DVTFM ACLP NMIVMAPSDE ADLFNMVATA VAIDDRPSCF RYPRGNGIGV ALPPGNKGVP IEIGKGRILK EGERVALLGY GSAVQS CLG AAVMLEERGL NVTVADARFC KPLDRALIRS LAKSHEVLIT VEEGSIGGFG SHVVQFLALD GLLDGKLKWR PMVLPDR YI DHGAPADQLA EAGLMPSHIA ATALNLIGAP REALFHHHHH HDYKDDDDK

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Macromolecule #2: Heat shock protein 21, chloroplastic

MacromoleculeName: Heat shock protein 21, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.654545 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSENLY FQSAQDQREN SIDVVQQGQQ KGNQGSSVEK RPQQRLTMDV SPFGLLDPLS PMRTMRQMLD TMDRMFEDT MPVSGRNRGG SGVSEIRAPW DIKEEEHEIK MRFDMPGLSK EDVKISVEDN VLVIKGEQKK EDSDDSWSGR S VSSYGTRL ...String:
MGSSHHHHHH SQDPNSENLY FQSAQDQREN SIDVVQQGQQ KGNQGSSVEK RPQQRLTMDV SPFGLLDPLS PMRTMRQMLD TMDRMFEDT MPVSGRNRGG SGVSEIRAPW DIKEEEHEIK MRFDMPGLSK EDVKISVEDN VLVIKGEQKK EDSDDSWSGR S VSSYGTRL QLPDNCEKDK IKAELKNGVL FITIPKTKVE RKVIDVQIQ

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initio from RELION 3.0
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162426

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