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- EMDB-31171: CrClpP-S1 -

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Basic information

Entry
Database: EMDB / ID: EMD-31171
TitleCrClpP-S1
Map datathe 3.3 angstrom resolution cryo-EM density map of CrClp protease complex in Chlamydomonas reinhardtii.
Sample
  • Complex: complex of CrClp protease
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic
KeywordsClp / Complex / Protease / Chloroplast / Chlamydomnas / Atp-dependent. / STRUCTURAL PROTEIN
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / chloroplast stroma / plastid / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chloroplast / ATPase binding / serine-type endopeptidase activity
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / Clp, N-terminal domain superfamily / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang N / Wang YF
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-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eko
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31171.png

Downloads & links

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Map

FileDownload / File: emd_31171.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe 3.3 angstrom resolution cryo-EM density map of CrClp protease complex in Chlamydomonas reinhardtii.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 216 pix.
= 284.688 Å		1.32 Å/pix.
x 216 pix.
= 284.688 Å		1.32 Å/pix.
x 216 pix.
= 284.688 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: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.14222087 - 0.25759324
Average (Standard dev.)0.00035640135 (±0.006711604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 284.688 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z284.688284.688284.688
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1420.2580.000

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Supplemental data

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Sample components

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Entire : complex of CrClp protease

EntireName: complex of CrClp protease
Components
  • Complex: complex of CrClp protease
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease proteolytic subunit
    • Protein or peptide: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic

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Supramolecule #1: complex of CrClp protease

SupramoleculeName: complex of CrClp protease / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 549.4 kDa/nm

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Macromolecule #1: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 26.571436 KDa
SequenceString: RRNVEARGIR RSPVVTPDIQ IGHGEDAIEM DLYRYLLSNR IIFIGGYIND KMATQIVGSL MALEAVDENE DIRIYINSPG GQPYSVLGV VDAMQSIKPD VQTVALGACY SYASLVVAAG TKGKRYAMKN TRLMMTQPMG GSQGDIYQIK ATVEELNALY Q IFSRYYMK ...String:
RRNVEARGIR RSPVVTPDIQ IGHGEDAIEM DLYRYLLSNR IIFIGGYIND KMATQIVGSL MALEAVDENE DIRIYINSPG GQPYSVLGV VDAMQSIKPD VQTVALGACY SYASLVVAAG TKGKRYAMKN TRLMMTQPMG GSQGDIYQIK ATVEELNALY Q IFSRYYMK FTGMNQDQIE QATCRDHFMT PEQAKLEGLI DEIIRGKGDY TVPPAIVRQF REVGLVDDLT PGPFLKVDCN

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #2: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 25.815459 KDa
SequenceString: ARRSVAARSS APELWTPTSE VKLAVSSRNP HPPVVCQGPP PPNPLVIERF QGVVSQLFQQ RIVRLGGAVD DDMANLLVAQ LLYLDSVDN KRDITMYVNS PGGSVTAGMA VFDTMRHIRP DVSTCCIGLA ASMGAFILAS GQAGKRYSLP NSRIMIHQPL G GAQGQATD ...String:
ARRSVAARSS APELWTPTSE VKLAVSSRNP HPPVVCQGPP PPNPLVIERF QGVVSQLFQQ RIVRLGGAVD DDMANLLVAQ LLYLDSVDN KRDITMYVNS PGGSVTAGMA VFDTMRHIRP DVSTCCIGLA ASMGAFILAS GQAGKRYSLP NSRIMIHQPL G GAQGQATD IEIQANEILH HKLTLNGYLA QFTGQSMETI TKDTDRDFFM SPQEAIEYGL VDAIISKPQM LQSREVALSS

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #3: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 33.229863 KDa
SequenceString: NSQPIVAPRT AEMQGDPFGL LLRQRIVFLG GEVEDFGADA IISQLLLLDS QDPTKDIKIF INSPGGSVTA GMGIYDAMML CRADVNTYC FGLAASMGAF LLGAGKRGKR NSMPNSRIMI HQPLGGASGQ AVDIEIQAKE IMYHKANLNR IMADYCQQPL S KIEEDTDR ...String:
NSQPIVAPRT AEMQGDPFGL LLRQRIVFLG GEVEDFGADA IISQLLLLDS QDPTKDIKIF INSPGGSVTA GMGIYDAMML CRADVNTYC FGLAASMGAF LLGAGKRGKR NSMPNSRIMI HQPLGGASGQ AVDIEIQAKE IMYHKANLNR IMADYCQQPL S KIEEDTDR DRYMSPLEAK EYGLIDHIIG GEEAVFNVKG SLKKFPKIKE EFVTDKDDMV KRNIMDGDPF LSETPSWRFK SP QTEPYMP SQAPGSRWFR TRKVSKEDYK EMQEQRQAEL MAESDDGKKS VKDRIDDAW

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #4: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: endopeptidase Clp
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 23.105768 KDa
SequenceString: NYLDQGALNN ESGRSLYRKQ TERVIQEEES KKVFMIINSF GGSVGNGITV HDALQFIKAG SLTLALGVAA SAASLALAGG TIGERYVTE GCHTMIHQPE GGLNGQASDI WIDSQEIMKI RLDVAEIYSL STYRPRHKIL RDLDRDFYLT AMETIYYGLA D EIATNEVM ...String:
NYLDQGALNN ESGRSLYRKQ TERVIQEEES KKVFMIINSF GGSVGNGITV HDALQFIKAG SLTLALGVAA SAASLALAGG TIGERYVTE GCHTMIHQPE GGLNGQASDI WIDSQEIMKI RLDVAEIYSL STYRPRHKIL RDLDRDFYLT AMETIYYGLA D EIATNEVM HSIVEMTNQV WSYHDSKQER LLESRASLVG DSTQTQESNS

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #5: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.13601 KDa
SequenceString: AYGDYPNYPE GRPLFLPEAE RFGNPPDLPS LLLQQRVIYI SMPFLPSVTE LVVAQCYYLD FDDRNRQRPI YVYLNSTGCI NDKGQAISA DNEFYAIWAA LGFTRAPLYT GVTWKAQNQA AVLLSAGQKG HRYSFPHAKI STAPPVMNRV FGQAVDAQLQ A NELDYATK ...String:
AYGDYPNYPE GRPLFLPEAE RFGNPPDLPS LLLQQRVIYI SMPFLPSVTE LVVAQCYYLD FDDRNRQRPI YVYLNSTGCI NDKGQAISA DNEFYAIWAA LGFTRAPLYT GVTWKAQNQA AVLLSAGQKG HRYSFPHAKI STAPPVMNRV FGQAVDAQLQ A NELDYATK YYAAILARST GKDLETCQKQ YLSRKRYFSV KEAYEEGLVD KLVPGFMLNR FRKMQKDAGV GEEDLFDMNK PK FKFRRQ

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #6: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.381633 KDa
SequenceString: RKLSHLRKKL WKEAGPPPDL ATRLFSERIM YLGMPIDSSV AELLTAQLFV LVQEAPDPIF FYINSTGIAK STTKFGNEHE AIAVYSMMK GVQKYCPIYT LCVGNAFGEA ALLLSAGSPG KRAALRSSTI MLRQPLQRLG GMQASDIDIY RKITREKTAT M AKYLAACT ...String:
RKLSHLRKKL WKEAGPPPDL ATRLFSERIM YLGMPIDSSV AELLTAQLFV LVQEAPDPIF FYINSTGIAK STTKFGNEHE AIAVYSMMK GVQKYCPIYT LCVGNAFGEA ALLLSAGSPG KRAALRSSTI MLRQPLQRLG GMQASDIDIY RKITREKTAT M AKYLAACT KKTEEQIMTD FTRPRYFNPY EAVSYGLIDT VLEPKEERAV FKDWEKMGSE IADLGLWDDE EQPLPTNIMY PG TSQYWRS DFDG

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #7: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 28.345898 KDa
SequenceString: KKSPQGFWQV TTKQISAAKR SGAPKRKVTT MMPVSVPKVL CRPPGQRQSE WVDLWEAYTY QKVVFIKEAI TEDVANNMIA LTLYLDSLD QKRIYYWLNV PGGDVVPTLA LYDTMQYVRS KTATVCYGLC LGMGGFLLTA GGEKGYRFAM PHSILMMHHP S GASRGQAS ...String:
KKSPQGFWQV TTKQISAAKR SGAPKRKVTT MMPVSVPKVL CRPPGQRQSE WVDLWEAYTY QKVVFIKEAI TEDVANNMIA LTLYLDSLD QKRIYYWLNV PGGDVVPTLA LYDTMQYVRS KTATVCYGLC LGMGGFLLTA GGEKGYRFAM PHSILMMHHP S GASRGQAS EMHIESRELV RMRDYLSLLT SNATGQPYDR VIRELSRNKW MDPKQAIEYG MIDKVLTTPM PKMPSTGPSF KF ERQNDEL IGL

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #8: ATP-dependent Clp protease proteolytic subunit

MacromoleculeName: ATP-dependent Clp protease proteolytic subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 43.457613 KDa
SequenceString: LVVHARASRY DRRKPPPPDL PSLLFDQRIV YLGMPLVPAV TELMVAELLY LEKQGATLPI EMLINSSGTT RQDGEILSFD SEGVALTST MGFIKNPIST VNMGLAVGWS CVVLSFGRKG WRKSLPHSLA MIQQPRVPPT GQRQAIEVHI KWREVLDYKR E LLRMFSLG ...String:
LVVHARASRY DRRKPPPPDL PSLLFDQRIV YLGMPLVPAV TELMVAELLY LEKQGATLPI EMLINSSGTT RQDGEILSFD SEGVALTST MGFIKNPIST VNMGLAVGWS CVVLSFGRKG WRKSLPHSLA MIQQPRVPPT GQRQAIEVHI KWREVLDYKR E LLRMFSLG TGLPVDKLDA DMQRPLYMRP QDALEYGIID EIIEPNEDKA EKAAQYWIRS GRAESEGRLE QWQEYLSLQE EY ALKDSFR KVMTQDLRAA YRDTSSKLLK NSSRNMEQVQ EFKERLPDDM LTENDEVRLP FSRDGVKLAI LNAECYAERN IAR QVAANK VSVPDKWRAA YAARPAPAAP AAEVDYDALI RAVEAMDEKA FATTDLDTLV EQYRVPA

UniProtKB: ATP-dependent Clp protease proteolytic subunit

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Macromolecule #9: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic

MacromoleculeName: ATP-dependent Clp protease ATP-binding subunit CLPT4, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 19.869402 KDa
SequenceString:
ATATAAPSEL DDVGVSAAAE SIIQYAINFA RASETYEVHS WMVLMGILKY ETCTAAKILK SLGLEDLYGA WNEVLWALNV CDGLQPRSF VTDIKFADRA FKVITAASDF AVWHGKDKMY SEDVLMALAA GGVLEDLFPD LNLSFERVRK AVEKESGRRY Q LPDETEEA GPLKSEDDVS FL

UniProtKB: ATP-dependent Clp protease ATP-binding subunit CLPT4, 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
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131245
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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