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- EMDB-31173: CrClpP-S2c -

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Basic information

Entry
Database: EMDB / ID: EMD-31173
TitleCrClpP-S2c
Map dataThe 3.6 angstrom resolution cryo-EM density map of CrClp-cpn11/20/23 complex in Chlamydomonas reinhardtii.
Sample
  • Complex: complex of CrClp protease and co-chaperonin Cpn112023
    • Protein or peptide: x 12 types
Function / homology
Function and homology information


endopeptidase Clp complex / endopeptidase Clp / plastid / chloroplast stroma / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone cofactor-dependent protein refolding / chloroplast / unfolded protein binding / ATPase binding ...endopeptidase Clp complex / endopeptidase Clp / plastid / chloroplast stroma / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone cofactor-dependent protein refolding / chloroplast / unfolded protein binding / ATPase binding / protein-folding chaperone binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. ...Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / Clp, N-terminal domain superfamily / GroES-like superfamily / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
ATP-dependent Clp protease proteolytic subunit / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / Chaperonin 23 / 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 / Uncharacterized protein / ATP-dependent Clp protease proteolytic subunit / ATP-dependent Clp protease proteolytic subunit / Chaperonin 23 / 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 / Chaperonin 11 / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: 0.852
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.852
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ekq
  • Surface level: 0.852
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31173.png

Downloads & links

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Map

FileDownload / File: emd_31173.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe 3.6 angstrom resolution cryo-EM density map of CrClp-cpn11/20/23 complex in Chlamydomonas reinhardtii.
Voxel sizeX=Y=Z: 1.318 Å
Density
Contour LevelBy AUTHOR: 0.852 / Movie #1: 0.852
Minimum - Maximum-0.5398395 - 2.7356322
Average (Standard dev.)0.020675443 (±0.13802923)
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-0.5402.7360.021

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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: 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
    • Protein or peptide: Chaperonin 11
    • Protein or peptide: Chaperonin 23
    • Protein or peptide: Cpn20 co-chaperonin 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: 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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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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 smithii (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

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Macromolecule #10: Chaperonin 11

MacromoleculeName: Chaperonin 11 / type: protein_or_peptide / ID: 10 / 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 #11: Chaperonin 23

MacromoleculeName: Chaperonin 23 / type: protein_or_peptide / ID: 11 / 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 #12: Cpn20 co-chaperonin subunit

MacromoleculeName: Cpn20 co-chaperonin subunit / type: protein_or_peptide / ID: 12 / 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 chloridesodium chloride
20.0 mMTris-HClTrisTris base
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: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49759

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