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- EMDB-30262: DXPS -

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Basic information

Entry
Database: EMDB / ID: EMD-30262
TitleDXPS
Map data
Sample
  • Complex: Hsp21
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
Keywords1-deoxy-D-xylulose 5-phosphate synthase / PLANT PROTEIN / TRANSFERASE
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / chlorophyll biosynthetic process / thiamine biosynthetic process / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / chloroplast stroma / chloroplast / identical protein binding / metal ion binding
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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
1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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) releaseNov 17, 2021-
Map releaseNov 17, 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: 0.145
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.145
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bzx
  • Surface level: 0.145
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30262.png

Downloads & links

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Map

FileDownload / File: emd_30262.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 192 pix.
= 197.76 Å		1.03 Å/pix.
x 192 pix.
= 197.76 Å		1.03 Å/pix.
x 192 pix.
= 197.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145 / Movie #1: 0.145
Minimum - Maximum-0.21625046 - 0.6422063
Average (Standard dev.)0.003289123 (±0.025809644)
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/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2160.6420.003

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Supplemental data

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Sample components

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Entire : Hsp21

EntireName: Hsp21
Components
  • Complex: Hsp21
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase, 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: 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

UniProtKB: 1-deoxy-D-xylulose-5-phosphate synthase, 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128927
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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