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- EMDB-31174: Cpn11/20/23 -

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Basic information

Entry
Database: EMDB / ID: EMD-31174
TitleCpn11/20/23
Map data
Sample
  • Complex: complex of CrClp protease and co-chaperonin Cpn112023
    • Protein or peptide: Chaperonin 11
    • Protein or peptide: Chaperonin 23
    • Protein or peptide: Cpn20 subunit
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsWang N / Wang YF / Cong Y / Liu CM
CitationJournal: Nat Plants / Year: 2021
Title: The cryo-EM structure of the chloroplast ClpP complex.
Authors: Ning Wang / Yifan Wang / Qian Zhao / Xiang Zhang / Chao Peng / Wenjuan Zhang / Yanan Liu / Olivier Vallon / Michael Schroda / Yao Cong / Cuimin Liu /
Abstract: Protein homoeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. Here, we determined the ...Protein homoeostasis in plastids is strategically regulated by the protein quality control system involving multiple chaperones and proteases, among them the Clp protease. Here, we determined the structure of the chloroplast ClpP complex from Chlamydomonas reinhardtii by cryo-electron microscopy. ClpP contains two heptameric catalytic rings without any symmetry. The top ring contains one ClpR6, three ClpP4 and three ClpP5 subunits while the bottom ring is composed of three ClpP1 subunits and one each of the ClpR1-4 subunits. ClpR3, ClpR4 and ClpT4 subunits connect the two rings and stabilize the complex. The chloroplast Cpn11/20/23 co-chaperonin, a co-factor of Cpn60, forms a cap on the top of ClpP by protruding mobile loops into hydrophobic clefts at the surface of the top ring. The co-chaperonin repressed ClpP proteolytic activity in vitro. By regulating Cpn60 chaperone and ClpP protease activity, the co-chaperonin may play a role in coordinating protein folding and degradation in the chloroplast.
History
DepositionApr 6, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateMay 4, 2022-
Current statusMay 4, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.83
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.83
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31174.png

Downloads & links

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Map

FileDownload / File: emd_31174.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 96 pix.
= 126.528 Å		1.32 Å/pix.
x 96 pix.
= 126.528 Å		1.32 Å/pix.
x 96 pix.
= 126.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.83 / Movie #1: 0.83
Minimum - Maximum-1.9449328 - 2.6505241
Average (Standard dev.)0.02904285 (±0.19663824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 126.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z126.528126.528126.528
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-1.9452.6510.029

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Supplemental data

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Sample components

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Entire : complex of CrClp protease and co-chaperonin Cpn112023

EntireName: complex of CrClp protease and co-chaperonin Cpn112023
Components
  • Complex: complex of CrClp protease and co-chaperonin Cpn112023
    • Protein or peptide: Chaperonin 11
    • Protein or peptide: Chaperonin 23
    • Protein or peptide: Cpn20 subunit

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Supramolecule #1: complex of CrClp protease and co-chaperonin Cpn112023

SupramoleculeName: complex of CrClp protease and co-chaperonin Cpn112023 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Chaperonin 11

MacromoleculeName: Chaperonin 11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 10.953762 KDa
SequenceString:
AASVTAEKAA LDITKMTPIH DRVLIRPIEE EQKTAGGILL PKAPPKANSD AHIGEVLAVG SDVTLAVAKG DMVVFQKYAM AEVEVKEGQ IIFVAEKSIM GKLE

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Macromolecule #2: Chaperonin 23

MacromoleculeName: Chaperonin 23 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 23.061414 KDa
SequenceString: EAISVPAPFT KVAPKGDRVL VKVAEEEVKT RGGILLPPSA IKKPTSGEVV QLGDGRVGDG EVRPFYLQPG QTVVYSKFGF MYQDLKLSN GEEYILIRED DVIGIMPRAN AQADDVPELQ PLADRVLIKV EEVADVTMGG VFLPETAKER PLSGTVVRVG P GKYDKDAE ...String:
EAISVPAPFT KVAPKGDRVL VKVAEEEVKT RGGILLPPSA IKKPTSGEVV QLGDGRVGDG EVRPFYLQPG QTVVYSKFGF MYQDLKLSN GEEYILIRED DVIGIMPRAN AQADDVPELQ PLADRVLIKV EEVADVTMGG VFLPETAKER PLSGTVVRVG P GKYDKDAE GKRRTVPLAP GDKVLYFKYA GDNMETPSGD KFVVLRSDDV LCKA

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Macromolecule #3: Cpn20 subunit

MacromoleculeName: Cpn20 subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 20.480365 KDa
SequenceString: ATPVPKQFKA VKPVGDRVLV KVDKEEAKSV GGVLLPASVR NKPTAGSIIA LGDAKSVKLS DKVIYSKFAG TELELGGAEH VLLKEEDVI GVLSASEKIA QLKPLSDRIL IKGAKAEDKT SGGVLLATES AEKPTFGTVV AVGEGREDEE TKALVKPNVT V GATVMYSK ...String:
ATPVPKQFKA VKPVGDRVLV KVDKEEAKSV GGVLLPASVR NKPTAGSIIA LGDAKSVKLS DKVIYSKFAG TELELGGAEH VLLKEEDVI GVLSASEKIA QLKPLSDRIL IKGAKAEDKT SGGVLLATES AEKPTFGTVV AVGEGREDEE TKALVKPNVT V GATVMYSK YSGTEFEEDG DNYIVVRESD ILAQLS

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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
Component:
ConcentrationFormulaName
80.0 mMNaClsodium chloride
20.0 mMTris-HClTris base
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13040
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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