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- EMDB-38428: Cryo-EM structure of the Ycf2-FtsHi motor complex from Arabidopsi... -

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Basic information

Entry
Database: EMDB / ID: EMD-38428
TitleCryo-EM structure of the Ycf2-FtsHi motor complex from Arabidopsis in Apo state
Map data
Sample
  • Complex: The Ycf2-FtsHi motor complex from Arabidopsis
    • Protein or peptide: x 16 types
  • Ligand: x 2 types
KeywordsATP-motor / Ycf2 / FtsHi / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of photorespiration / chloroplast protein-transporting ATPase activity / Ycf2/FtsHi complex / plastid stroma / plastid fission / protein import into chloroplast stroma / chloroplast inner membrane / stromule / chloroplast fission / chloroplast membrane ...regulation of photorespiration / chloroplast protein-transporting ATPase activity / Ycf2/FtsHi complex / plastid stroma / plastid fission / protein import into chloroplast stroma / chloroplast inner membrane / stromule / chloroplast fission / chloroplast membrane / chloroplast organization / malate dehydrogenase / embryo development ending in seed dormancy / L-malate dehydrogenase (NAD+) activity / malate metabolic process / plasmodesma / apoplast / plant-type vacuole / chloroplast envelope / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / plastid / chloroplast stroma / ATP-dependent peptidase activity / chloroplast thylakoid membrane / tricarboxylic acid cycle / response to cold / cell redox homeostasis / chloroplast / metalloendopeptidase activity / defense response to bacterium / ATP hydrolysis activity / mitochondrion / proteolysis / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Uncharacterised protein family Ycf2 / Plant protein of unknown function (DUF825) / : / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Lactate/malate dehydrogenase, N-terminal ...Uncharacterised protein family Ycf2 / Plant protein of unknown function (DUF825) / : / Peptidase M41 / Peptidase M41-like / Peptidase family M41 / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / NAD(P)-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic / Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic / Embryo defective 2737 / Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic / Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic / Protein Ycf2 / Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B / At4g28210 / ATP-dependent zinc metalloprotease FTSH 12, chloroplastic / Malate dehydrogenase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiang K / Zhan X / Xu Q / Wu J / Yan Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271239 China
CitationJournal: Cell / Year: 2024
Title: Structural insights into the chloroplast protein import in land plants.
Authors: Ke Liang / Zeyu Jin / Xiechao Zhan / Yuxin Li / Qikui Xu / Yanqiu Xie / Yi Yang / Shaojie Wang / Jianping Wu / Zhen Yan /
Abstract: Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi ...Chloroplast proteins are imported via the translocon at the outer chloroplast membrane (TOC)-translocon at the inner chloroplast membrane (TIC) supercomplex, driven by an ATPase motor. The Ycf2-FtsHi complex has been identified as the chloroplast import motor. However, its assembly and cooperation with the TIC complex during preprotein translocation remain unclear. Here, we present the structures of the Ycf2-FtsHi and TIC complexes from Arabidopsis and an ultracomplex formed between them from Pisum. The Ycf2-FtsHi structure reveals a heterohexameric AAA+ ATPase motor module with characteristic features. Four previously uncharacterized components of Ycf2-FtsHi were identified, which aid in complex assembly and anchoring of the motor module at a tilted angle relative to the membrane. When considering the structures of the TIC complex and the TIC-Ycf2-FtsHi ultracomplex together, it becomes evident that the tilted motor module of Ycf2-FtsHi enables its close contact with the TIC complex, thereby facilitating efficient preprotein translocation. Our study provides valuable structural insights into the chloroplast protein import process in land plants.
History
DepositionDec 25, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38428.png

Downloads & links

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Map

FileDownload / File: emd_38428.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.63382 - 4.9598417
Average (Standard dev.)0.008739842 (±0.08575107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38428_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38428_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : The Ycf2-FtsHi motor complex from Arabidopsis

EntireName: The Ycf2-FtsHi motor complex from Arabidopsis
Components
  • Complex: The Ycf2-FtsHi motor complex from Arabidopsis
    • Protein or peptide: ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
    • Protein or peptide: Malate dehydrogenase, chloroplastic
    • Protein or peptide: Protein Ycf2
    • Protein or peptide: Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic
    • Protein or peptide: Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic
    • Protein or peptide: Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic
    • Protein or peptide: AtTam46
    • Protein or peptide: Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic
    • Protein or peptide: Embryo defective 2737
    • Protein or peptide: At4g28210
    • Protein or peptide: Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B
    • Protein or peptide: UNK
    • Protein or peptide: UNK
    • Protein or peptide: UNK
    • Protein or peptide: UNK
    • Protein or peptide: UNK
  • Ligand: ZINC ION
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Supramolecule #1: The Ycf2-FtsHi motor complex from Arabidopsis

SupramoleculeName: The Ycf2-FtsHi motor complex from Arabidopsis / type: complex / ID: 1 / Parent: 0
Macromolecule list: #2, #9, #4, #1, #5, #3, #7, #6, #16, #8, #10, #13, #12, #11, #14-#15
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chl...

MacromoleculeName: Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 96.975398 KDa
SequenceString: MTFYISSSLT PTHFSKPLNP SNTLFPSQFR GSLSSFVRRR KPTEAKLSSK FNLFPSRRNG LITCCSTSSF ESTESSVSQE EDAESNRLF EKLRETERER LSNMEELERK ANVQLERQLV MASDWSRTLL TMRGKLKGTE WDPETSHRIN FSDFMKLLDS N SVQYMEYS ...String:
MTFYISSSLT PTHFSKPLNP SNTLFPSQFR GSLSSFVRRR KPTEAKLSSK FNLFPSRRNG LITCCSTSSF ESTESSVSQE EDAESNRLF EKLRETERER LSNMEELERK ANVQLERQLV MASDWSRTLL TMRGKLKGTE WDPETSHRIN FSDFMKLLDS N SVQYMEYS NYGQTISVIL PYYKDGEPLG EEEDSKKEII FRRHIVDRMP IDGWNDVWKK LHQQIVNVEV FNVDVVPAEV YT TVATFVV WSMRLALFVS LYVWIDSITR PIYAKLIPCD LGTPTKKIRQ PLKRQALGSL GKSRAKFISA EEKTGVTFDD FAG QEYIKR ELQEIVRILK NDEEFQNKGI YCPKGVLLHG PPGTGKTLLA KAIAGEAGLP FFAANGTDFV EMFVGVAASR VKDL FASSR SYAPSIIFID EIDAIGSKRG GPDIGGGGAE REQGLLQILT EMDGFKVTTS QVLVIGATNR LDILDPALLR KGRFD KIIR VGLPSKDGRL AILKVHARNK FFRSEDEKEE LLQEVAENTE DFTGAELQNV LNEAGILTAR KDLDYIGREE LLEALK RQK GTFETGQEDS TEVPEELKLR LAYREAAVAV LACYLPDQYR PISETDINSI RSQPNMRYSE TSGRVFARKS DYVNSII RA CAPRVVEEEM FGIENLCWIS AKSTLEASQR AEFLILQTGM TAFGKAYYRN QRDLVPNLVP KLEALRDEYM RFAVEKCS S ILQEYQSALE EITDVLLEKG EIKADEIWNI YNTAPRIPQK PVRPVDEYGA LIYAGRWGIH GVSLPGRVTF SPGNIGFAT FGAPRPMETQ IISDDTWKLV DEIWDKKVEE IKAEAVIQIE EEKKKPQILM ATHFF

UniProtKB: Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic

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Macromolecule #2: ATP-dependent zinc metalloprotease FTSH 12, chloroplastic

MacromoleculeName: ATP-dependent zinc metalloprotease FTSH 12, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 115.267148 KDa
SequenceString: MEIAISYKPN PLISSSTQLL KRSKSFGLVR FPAKYGLGAT RKKQLFRVYA SESSSGSSSN SDGGFSWVRL AQSIRLGAER IGEKIGESV KTEIGFDSEE ASGRVNEYVA RVKDSVHKGH HELTRFKNET VPSFIDWNKW EHWKDIRNWD GKRVAALFIY A FALLLSCQ ...String:
MEIAISYKPN PLISSSTQLL KRSKSFGLVR FPAKYGLGAT RKKQLFRVYA SESSSGSSSN SDGGFSWVRL AQSIRLGAER IGEKIGESV KTEIGFDSEE ASGRVNEYVA RVKDSVHKGH HELTRFKNET VPSFIDWNKW EHWKDIRNWD GKRVAALFIY A FALLLSCQ RVYVAIQAPR VERERRELTE SFMEALIPEP SPGNIEKFKR NMWRKATPKG LKLKRFIEAP DGTLVHDSSY VG ENAWDDD LETTEGSLKK IIGRNARIQT EAKKKLSQDL GVSGEIGDSV GNWRERLATW KEMLEREKLS EQLNSSAAKY VVE FDMKEV EKSLREDVIG RTSETEGTRA LWISKRWWRY RPKLPYTYFL QKLDSSEVAA VVFTEDLKRL YVTMKEGFPL EYIV DIPLD PYLFETICNA GVEVDLLQKR QIHYFMKVFI ALLPGILILW FIRESAMLLL ITSKRFLYKK YNQLFDMAYA ENFIL PVGD VSETKSMYKE VVLGGDVWDL LDELMIYMGN PMQYYEKDVA FVRGVLLSGP PGTGKTLFAR TLAKESGLPF VFASGA EFT DSEKSGAAKI NEMFSIARRN APAFVFVDEI DAIAGRHARK DPRRRATFEA LIAQLDGEKE KTGIDRFSLR QAVIFIC AT NRPDELDLEF VRSGRIDRRL YIGLPDAKQR VQIFGVHSAG KNLAEDIDFG KLVFRTVGFS GADIRNLVNE AAIMSVRK G RSYIYQQDIV DVLDKQLLEG MGVLLTEEEQ QKCEQSVSYE KKRLLAVHEA GHIVLAHLFP RFDWHAFSQL LPGGKETAV SVFYPREDMV DQGYTTFGYM KMQMVVAHGG RCAERVVFGD NVTDGGKDDL EKITKIAREM VISPQSARLG LTQLVKKIGM VDLPDNPDG ELIKYRWDHP HVMPAEMSVE VSELFTRELT RYIEETEELA MNALRANRHI LDLITRELLE KSRITGLEVE E KMKDLSPL MFEDFVKPFQ INPDDEELLP HKDRVSYQPV DLRAAPLHRS

UniProtKB: ATP-dependent zinc metalloprotease FTSH 12, chloroplastic

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Macromolecule #3: Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chl...

MacromoleculeName: Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 152.4795 KDa
SequenceString: MDFISASSLS SPFSTQLSPI YLSSGIVSLK PRHRVKNRNF GSRESNNKSR KIVPIRGCFG FSGSFLRSKQ SDYGSEAVSE SLRLCGEGN ELVLSSEYNS AKTRESVIQF VTKPLVYALF CIAIGLSPIR SFQAPALAVP FVSDVIWKKK KERVREKEVV L KAVDHEFS ...String:
MDFISASSLS SPFSTQLSPI YLSSGIVSLK PRHRVKNRNF GSRESNNKSR KIVPIRGCFG FSGSFLRSKQ SDYGSEAVSE SLRLCGEGN ELVLSSEYNS AKTRESVIQF VTKPLVYALF CIAIGLSPIR SFQAPALAVP FVSDVIWKKK KERVREKEVV L KAVDHEFS DYTRRLLETV SVLLKTIEIV RKENGEVAEV GAALDAVKVE KEKLQKEIMS GLYRDMRRLR KERDLLMKRA DK IVDEALS LKKQSEKLLR KGAREKMEKL EESVDIMESE YNKIWERIDE IDDIILKKET TTLSFGVREL IFIERECVEL VKS FNRELN QKSFESVPES SITKLSRSEI KQELVNAQRK HLEQMILPNV LELEEVDPFF DRDSVDFSLR IKKRLEESKK LQRD LQNRI RKRMKKFGEE KLFVQKTPEG EAVKGFPEAE VKWMFGEKEV VVPKAIQLHL RHGWKKWQEE AKADLKQKLL EDVDF GKQY IAQRQEQVLL DRDRVVSKTW YNEDKSRWEM DPMAVPYAVS RKLIDSARIR HDYAVMYVAL KGDDKEFYVD IKEYEM LFE KFGGFDALYL KMLACGIPTS VHLMWIPMSE LSLQQQFLLV TRVVSRVFNA LRKTQVVSNA KDTVLEKIRN INDDIMM AV VFPVIEFIIP YQLRLRLGMA WPEEIEQTVG STWYLQWQSE AEMNFKSRNT EDFQWFLWFL IRSSIYGFVL YHVFRFLK R KVPRLLGYGP FRRDPNVRKF WRVKSYFTYR KRRIKQKRKA GIDPIKTAFD RMKRVKNPPI PLKNFASIES MREEINEVV AFLQNPKAFQ EMGARAPRGV LIVGERGTGK TSLALAIAAE ARVPVVNVEA QELEAGLWVG QSAANVRELF QTARDLAPVI IFVEDFDLF AGVRGKFVHT KQQDHESFIN QLLVELDGFE KQDGVVLMAT TRNHKQIDEA LRRPGRMDRV FHLQSPTEME R ERILHNAA EETMDRELVD LVDWRKVSEK TTLLRPIELK LVPMALESSA FRSKFLDTDE LLSYVSWFAT FSHIVPPWLR KT KVAKTMG KMLVNHLGLN LTKDDLENVV DLMEPYGQIS NGIELLNPTV DWTRETKFPH AVWAAGRALI TLLIPNFDVV ENL WLEPSS WEGIGCTKIT KVTSGGSAIG NTESRSYLEK KLVFCFGSHI ASQMLLPPGD ENFLSSSEIT KAQEIATRMV LQYG WGPDD SPAVYYATNA VSALSMGNNH EYEMAGKVEK IYDLAYEKAK GMLLKNRRVL EKITEELLEF EILTHKDLER IVHEN GGIR EKEPFFLSGT NYNEALSRSF LDVGDPPETA LLSAPT

UniProtKB: Probable inactive ATP-dependent zinc metalloprotease FTSHI 5, chloroplastic

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Macromolecule #4: Protein Ycf2

MacromoleculeName: Protein Ycf2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 269.925719 KDa
SequenceString: MKGHQFKSWI FELREIVREI KNAHYFLDSW TQFNSVGSFI HIFFHQERFR KLLDPRIFSI LLLRNSQGST SNRYFTIKGV VLFVVAALL YRINNRNMVE SKNLYLKGLL PIPMNSIGPR NDTSEESFGS CNINRLIVSL LYLTKGKKIS ESCFRDPKES T WVLPITQK ...String:
MKGHQFKSWI FELREIVREI KNAHYFLDSW TQFNSVGSFI HIFFHQERFR KLLDPRIFSI LLLRNSQGST SNRYFTIKGV VLFVVAALL YRINNRNMVE SKNLYLKGLL PIPMNSIGPR NDTSEESFGS CNINRLIVSL LYLTKGKKIS ESCFRDPKES T WVLPITQK CIMPESNWSS RWWRNWIGKK RGFCCKISNE TVAGIDISFK EKDIKYLEFL FVYYMDDPIR KGHDWELFDR LS PSKRRNI INLNSGQLFE ILVKDWICYL MFAFREKIPI EVEGFCKQQG AGSTIQSNDI EHVSHLFSRN KWAISLQNCA QFH MWQFHQ DLFVSWGKNP HESDFFRKIS RENWIWLDNV WLVNKDRFFS KVRNVSSNIQ YDSTRSSFVQ VTDSSQLNGS SDQF IDPFD SISNEDSEYH YHTLINQREI QQLKERSILL DPSFIQTEGR EIESDRFPKY LSGYSSMPRL FTEREKRMNN HLLPE ESEE FLGNPTRAIR SFFSDRWSEL HLGSNPTERS TRDQKLLKKE QDVSFVPSRR SENKEIVNIF KIITYLQNTV SIHPIS SDL GCDMVPKDEL DMDSSNKISF LNKNPFFDLF HLFHERKRGG YTLRHESEER FQEMADLFTL SITEPDLVYH KGFAFSI DS YGLDQRQFLK EVFNFRDESK KKSLLVLPPI FYEENESFYR RLRKIWVRIS CGNYLEDQKR VVFASNNIME AVNQYRLI R NMIQIQFQYS PYGYIRNVLN RFFLMKRPDR NFEYGIQRDL IGNDTLNHRT IMKDTINQHL SNLKKSQKKW FDPLIFLSQ TERSINRDPN AYRYKWSNGS KNFQEHLEHF VSERKSRFQV VFDQLCINQY SIDWSEVIDK KDLSKSLRFF LSKLLRFFLS KLLLFLSKL LLFLSNSLPF FFVSFENIPI HRSEIHIYEL KGPNDQLCNQ LLESIGLQIV HLKKLKPFLL DDHNTSQKSK F LINGGTIS PFLFNKIPKW MIDSFHTRKN RRKSFDNTDS AYFSIVSHDQ DNWLNPVKPF QRSSLISSFS KANRLRFLNN PH HFCFYCN KRFPFYVEKA RLNNSDFTFT YGQFLTILFI HNKTFSSCGG KKKHAFLERD TISPSSIESQ VSNIFISNDF PQS GDERYN LYKSFHFPIR SDPLVRRAIY SIADISGTPL IEGQRVNFER TYCQTLSDMN LSDSEEKSLH QYLNFNSNMG LIHT PCSEK YLQRKKRSLC LKKCVDKGQM DRTFQRDSAF STLSKWNLFQ TYMPWFFTST GYKYLNLIFL DTFSDLLRIL SSSQK FVSI FHDIMHGLDI SWRILQKKLC LPQRNLISEI SSKSLHNLLL SEEMIHRNNE SSLISTHLRS PNVREVLYSI LFLLLV AGY IVRTHLLFVS RAYSELQTEF EKIKSLMIPS YMIELRKLLD RYPTSELNSF WLKNLFLVAL EQLGDCLEEI RGSGGNM LW GGDPAYGVKS IRSKKKDLKI NFIDIIDLIS IIPNPINRIT FSRNTRHLSH TSKEIYSLIR KRKNVSGDWI DDKIESWV A NSDSIDDKER EFLVQFSTLR AEKRIDQILL SLTHSDHLSK NDSGYQMIEQ PGTIYLRYLV DIHKKYLMNY EFNTSCLAE RRIFLAHYQT ITYSQTSCGA NSFHFPSHGK PFSLRLALSP SRSILVIGSI GTGRSYLVKY LATNSYVPFI TVFLNKFLDN KPKGFFIDD IDIDDSDDID ASNDIDRELD TELELLTMMN ALTMDMMLEI DRFYITLQFE LAKAMSPCII WIPNIHDLDV N ESSYLALG LLVNSLSRDC ERCSTRNILV IASTHIPQKV DPALIAPNKL NTCIKIRRLL IPQQRKHFFT LSYTRGFHLE KK MFHTNGF ESITMGSSAR DLVALTNEAL SISITQKKSI IDTNTIRSAL HRQTWDLRSQ VRSVQDHGIL FYQIGRAVAQ NVL ISNCPI DPISIYMKKK SCNEGDSYLY KWYFELGTSM KKFTILLYLL SCSAGSVAQD LWSLPVPDEK NRITSYGFVE NDSD LVHGL LEVQGALVGS SRTEKDCSQF DNDRVTLLFR SEPRDPLYMM QDGSCSIVDQ RFLYEKYESE FEEGEGEGVL DPQQI EEDL FNHIVWAPRI WRPRGFLFDC IERPNELGFP YSAGSFRGKR IIYDEKYELQ ENDSEFLQSG TMQYQRRDRS SKEQGF FRI SQFIWDPADP LFFLFKDQPF VSVFSHREFF ADEEMSKGLL TSQTDPPTSI YKRWFIKNTQ EKHFELLIQR QRWLRTN SS LSNGFFRSNT RSESYQYLSN LFISNGTLLD RMTKTLLKKR WLFSDEMKIG FM

UniProtKB: Protein Ycf2

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Macromolecule #5: Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chl...

MacromoleculeName: Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 105.677828 KDa
SequenceString: MASIDNVFSL GTRFSIPENP KRSILKHATT SSFSARTQTR WRAPILRRSF TVLCELKTGS SSSGETNNSP AADDFVTRVL KENPSQVEP RYRVGDKLYN LKEREDLSKG TNAATGAFEF IKRKFDSKKK TETDKSEESV YLSDILREYK GKLYVPEQVF G PELSEEEE ...String:
MASIDNVFSL GTRFSIPENP KRSILKHATT SSFSARTQTR WRAPILRRSF TVLCELKTGS SSSGETNNSP AADDFVTRVL KENPSQVEP RYRVGDKLYN LKEREDLSKG TNAATGAFEF IKRKFDSKKK TETDKSEESV YLSDILREYK GKLYVPEQVF G PELSEEEE FEKNVKDLPK MSLEDFRKAM ENDKVKLLTS KEVSGVSYTS GYRGFIVDLK EIPGVKSLQR TKWSMKLEVG EA QALLKEY TGPQYEIERH MTSWVGKVAD FPNPVASSIS SRVMVELGMV TAVIAAAAVV VGGFLASAVF AVTSFAFVTT VYV VWPIAK PFLKLFVGVF LGVLEKSWDY IVDVLADGGI FSRISDFYTF GGVASSLEML KPILLVVMTM VLLVRFTLSR RPKN FRKWD LWQGIAFSQS KAEARVDGST GVKFADVAGI DEAVDELQEL VKYLKNPDLF DKMGIKPPHG VLLEGPPGCG KTLVA KAIA GEAGVPFYQM AGSEFVEVLV GVGSARIRDL FKRAKVNKPS VIFIDEIDAL ATRRQGIFKE NSDQLYNAAT QERETT LNQ LLIELDGFDT GKGVIFLGAT NRRDLLDPAL LRPGRFDRKI RVRPPNAKGR LDILKIHASK VKMSDSVDLS SYASNLP GW SGAKLAQLVQ EAALVAVRKT HNSILQSDMD DAVDRLTVGP TRIGLELGHQ GQCRRATTEV GVAITSHLLL RYENAKIE R CDRVSIIPRG QTLSQVVFHR LDDESYMFGR LPQLLHRLQV LLGGRAAEEV IYGSDTSKAS VDYLSDASWL ARKILTIWN LENPMVIHGE PPPWRKRPQF VGPRLDFEGS LYDDYDLVEP PVNFNMDDEV AHRSEELISQ MYNKTVSLLR QNQTALLKTV KVLLNQKEI SGEAIDFILD HYPPQTPLNS LLQEQNPGSL PFVPEHLRRE SGDFVLVNHS TDVNAQV

UniProtKB: Probable inactive ATP-dependent zinc metalloprotease FTSHI 1, chloroplastic

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Macromolecule #6: Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chl...

MacromoleculeName: Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 100.019688 KDa
SequenceString: MACRFPLHSS SPSQFLSPEN RQRLPRNYPS ISCQNNSATN VVHEDGDDND KAKTNQVNLL AIPITLTIIS ASLAKPSFAA AKVTERKRT QKKPQEALTL EQLKAWSKDL PVVSNRIPYT DILSLKAEGK LKHVIKPPNL SLRQKAEPVL VVLEDSRVLR T VLPSLEGN ...String:
MACRFPLHSS SPSQFLSPEN RQRLPRNYPS ISCQNNSATN VVHEDGDDND KAKTNQVNLL AIPITLTIIS ASLAKPSFAA AKVTERKRT QKKPQEALTL EQLKAWSKDL PVVSNRIPYT DILSLKAEGK LKHVIKPPNL SLRQKAEPVL VVLEDSRVLR T VLPSLEGN KRFWEQWDEL GIDVQCVNAY TPPVKRPPVP SPYLGFLWKV PAYMLTWVKP KKESKRAAEL KRMREDFKRQ RK EEIETMK EERVMMEKTM KAQKKQQERK KRKAVRKKKY EESLREARKN YRDMADMWAR LAQDPNVATA LGLVFFYIFY RVV VLNYRK QKKDYEDRLK IEKAEADERK KMRELEREME GIEEEDEEVE EGTGEKNPYL QMAMQFMKSG ARVRRASNKR LPEY LERGV DVKFTDVAGL GKIRLELEEI VKFFTHGEMY RRRGVKIPGG ILLCGPPGVG KTLLAKAVAG EAGVNFFSIS ASQFV EIYV GVGASRVRAL YQEARENAPS VVFIDELDAV GRERGLIKGS GGQERDATLN QLLVSLDGFE GRGEVITIAS TNRPDI LDP ALVRPGRFDR KIFIPKPGLI GRMEILQVHA RKKPMAEDLD YMAVASMTDG MVGAELANIV EIAAINMMRD GRTELTT DD LLQAAQIEER GMLDRKDRSL ETWRQVAINE AAMAVVAVNF PDMKNIEFLT INPRAGRELG YVRVKMDHIK FKEGMLSR Q SILDHITVQL APRAADELWY GEDQLSTIWA ETSDNARSAA RSLVLGGLSD KHHGLNNFWV ADRINDIDVE ALRILNMCY ERAKEILGRN RTLMDEVVEK LVQKKSLTKQ EFFTLVELYG SSKPMPPSIL ELRKIKRLEL EEMVLKLDMT TARNSS

UniProtKB: Probable inactive ATP-dependent zinc metalloprotease FTSHI 2, chloroplastic

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Macromolecule #7: AtTam46

MacromoleculeName: AtTam46 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 45.844582 KDa
SequenceString: MEAVLLCSKL VPRAASLEGN QKFSFRHLNK HLKCNSLRAD SRDTPLLRGF EAIKSPSIWS CAPFPVRKGS WVPPRCSISS STVSDSDNP FLSQFRTFSF GSMVKKVREL KVKPMDVVKL TLLLSILTVA AKKTLTLVLD PFFWMYFSWT WLFWPWFIAV G LAGYGIYC ...String:
MEAVLLCSKL VPRAASLEGN QKFSFRHLNK HLKCNSLRAD SRDTPLLRGF EAIKSPSIWS CAPFPVRKGS WVPPRCSISS STVSDSDNP FLSQFRTFSF GSMVKKVREL KVKPMDVVKL TLLLSILTVA AKKTLTLVLD PFFWMYFSWT WLFWPWFIAV G LAGYGIYC FRKHWLGEAN AFEQLGIVTS VFTWLTLVPP AYFNGYLEGW PYVFFLAYHY FFFFNVSVRK RLYGDFYART HD PKWDVNT PLWSRILFGV GIMVGHWLAA FEGPELHRLP GGWANVGIWI LIVITMLMHY DSTLYLARYS EKVVVPTAVV QFG PYRWVR HPIYASTMLL FAAYCTALRA PLSLLFLLAV CLVYYNKKAK MEEELMVESF GQSYSDYADK VRHKFIPFVY

+
Macromolecule #8: At4g28210

MacromoleculeName: At4g28210 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.379551 KDa
SequenceString: MTLLALSSSL SSPSFFCRNS RIRFSPVSRI SSLNGDNKLT NSPPQFLNAG ASLRRFVAPG KFPSVRLRVL TRCEKENAPK GGIEDDAER FARRESTMPD RFRYLTKEAP DSPIIWPWFV ALGFLVYAWR AVLFELSNWR KAAFAILAFV GDLSKFALAL V FHFIGDPI ...String:
MTLLALSSSL SSPSFFCRNS RIRFSPVSRI SSLNGDNKLT NSPPQFLNAG ASLRRFVAPG KFPSVRLRVL TRCEKENAPK GGIEDDAER FARRESTMPD RFRYLTKEAP DSPIIWPWFV ALGFLVYAWR AVLFELSNWR KAAFAILAFV GDLSKFALAL V FHFIGDPI TSLISLVETA MYSVRAFYSG IVAYTPVREL TTVILLASSV LAIGEAVAPE SISKQPYVVT IAGLVGYAAV QS YISEPFF WTVLLGLYGY SRLIKKRDDV TSALPSAAVL AGVGEPWVRV VAITGYLALA MYHNSTKTSS EEESQILRRA PPM PLLAAA LAIGVRLAAK WAGYRHLTWM IV

UniProtKB: At4g28210

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Macromolecule #9: Malate dehydrogenase, chloroplastic

MacromoleculeName: Malate dehydrogenase, chloroplastic / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: malate dehydrogenase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 42.452449 KDa
SequenceString: MATATSASLF STVSSSYSKA SSIPHSRLQS VKFNSVPSFT GLKSTSLISG SDSSSLAKTL RGSVTKAQTS DKKPYGFKIN ASYKVAVLG AAGGIGQPLS LLIKMSPLVS TLHLYDIANV KGVAADLSHC NTPSQVRDFT GPSELADCLK DVNVVVIPAG V PRKPGMTR ...String:
MATATSASLF STVSSSYSKA SSIPHSRLQS VKFNSVPSFT GLKSTSLISG SDSSSLAKTL RGSVTKAQTS DKKPYGFKIN ASYKVAVLG AAGGIGQPLS LLIKMSPLVS TLHLYDIANV KGVAADLSHC NTPSQVRDFT GPSELADCLK DVNVVVIPAG V PRKPGMTR DDLFNINANI VKTLVEAVAE NCPNAFIHII SNPVNSTVPI AAEVLKKKGV YDPKKLFGVT TLDVVRANTF VS QKKNLKL IDVDVPVIGG HAGITILPLL SKTKPSVNFT DEEIQELTVR IQNAGTEVVD AKAGAGSATL SMAYAAARFV ESS LRALDG DGDVYECSFV ESTLTDLPFF ASRVKIGKNG LEAVIESDLQ GLTEYEQKAL EALKVELKAS IDKGVAFANK PAAA AAN

UniProtKB: Malate dehydrogenase, chloroplastic

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Macromolecule #10: Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B

MacromoleculeName: Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.327745 KDa
SequenceString:
MGNKATTVKE EREEIHLKIV PPLDKVFLRW LARDLQRVHG FKPKNNTRAI TPPDSYIEFM RLNGSLDVDL DDPDLAHLFK

UniProtKB: Aspartyl/glutamyl-tRNA (Asn/Gln) amidotransferase subunit B

+
Macromolecule #11: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.962466 KDa
SequenceString:
(UNK)FLNNLLKVM V(UNK)FL(UNK)(UNK)(UNK)(UNK)

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Macromolecule #12: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.232597 KDa
SequenceString:
(UNK)(UNK)VYVLVIKV K

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Macromolecule #13: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 3.781607 KDa
SequenceString:
(UNK)(UNK)V(UNK)(UNK)(UNK)LLN(UNK) VF(UNK)(UNK)(UNK)(UNK)L(UNK)HG R(UNK)(UNK)Q (UNK)(UNK)(UNK)(UNK)L YNLM(UNK)(UNK)F(UNK)

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Macromolecule #14: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.934522 KDa
SequenceString:
LTVLIKRGIL ILIHKKA

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Macromolecule #15: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #16: Embryo defective 2737

MacromoleculeName: Embryo defective 2737 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 37.382914 KDa
SequenceString: MSRGPGRLIQ NVTQFADAQF KQFSTRYGQQ VIDILDFPIK LVLSPFTLAF DIAGSAPRGF GIPEFISKIS YLSVFAVATL GTYDIALDL GKKVICQRDC KTCNGWQALR CTMCKGTGSV HYQIKDYNLR SGEKPTADCV ADAIVENRAE LVHLPSSFNH S APLPSKDC ...String:
MSRGPGRLIQ NVTQFADAQF KQFSTRYGQQ VIDILDFPIK LVLSPFTLAF DIAGSAPRGF GIPEFISKIS YLSVFAVATL GTYDIALDL GKKVICQRDC KTCNGWQALR CTMCKGTGSV HYQIKDYNLR SGEKPTADCV ADAIVENRAE LVHLPSSFNH S APLPSKDC PTCDGTGAMS CTECKNKLQV RISADDIMEP PWKAYNVLKK MDYPYEHIVH SMKDPSIANF WLITLPQIVG GF DYDEDVK KKIWWQYEES MRYDQLRDLV AKRNPGWEYL QDALVSIDPV RAREDPVIVK NVPYYKAKKS LEAESQKKAQ KGS RQRKWW FF

UniProtKB: Embryo defective 2737

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 340640
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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