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- EMDB-30261: Structure of Hsp21 -

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Basic information

Entry
Database: EMDB / ID: EMD-30261
TitleStructure of Hsp21
Map data
Sample
  • Complex: Hsp21
    • Protein or peptide: Heat shock protein 21, chloroplastic
Keywordssmall heat shock protein / CHAPERONE
Function / homology
Function and homology information


chloroplast nucleoid / chloroplast organization / protein folding chaperone complex / response to light stimulus / response to heat / regulation of DNA-templated transcription
Similarity search - Function
Heat shock protein 21-like / Hsp20/alpha crystallin family / Small heat shock protein (sHSP) domain profile. / Alpha crystallin/Hsp20 domain / HSP20-like chaperone
Similarity search - Domain/homology
Heat shock protein 21, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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 28, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bzw
  • Surface level: 0.0175
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30261.png

Downloads & links

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Map

FileDownload / File: emd_30261.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0175 / Movie #1: 0.0175
Minimum - Maximum-0.0047062016 - 0.049964543
Average (Standard dev.)0.00049398077 (±0.0025581706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ342342342
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0050.0500.000

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Supplemental data

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Additional map: Sharpened and filtered map

Fileemd_30261_additional_1.map
AnnotationSharpened and filtered map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_30261_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30261_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Hsp21

EntireName: Hsp21
Components
  • Complex: Hsp21
    • Protein or peptide: Heat shock protein 21, chloroplastic

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Supramolecule #1: Hsp21

SupramoleculeName: Hsp21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Heat shock protein 21, chloroplastic

MacromoleculeName: Heat shock protein 21, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 12 / 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

UniProtKB: Heat shock protein 21, chloroplastic

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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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104126
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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