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- EMDB-38799: Architecture of the spinach plastid-encoded RNA polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-38799
TitleArchitecture of the spinach plastid-encoded RNA polymerase
Map data
Sample
  • Complex: spinach plastid-encoded RNA polymerase
    • Protein or peptide: x 17 types
  • Ligand: x 1 types
Keywordsplastid-encoded RNA polymerase / chloroplast / spinach / TRANSCRIPTION
Function / homology
Function and homology information


etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid-encoded plastid RNA polymerase complex / plastid organization / thylakoid membrane organization / chloroplast nucleoid / acid-amino acid ligase activity / chloroplast organization / chloroplast thylakoid ...etioplast organization / plastid transcription / positive regulation of red or far-red light signaling pathway / plastid-encoded plastid RNA polymerase complex / plastid organization / thylakoid membrane organization / chloroplast nucleoid / acid-amino acid ligase activity / chloroplast organization / chloroplast thylakoid / thylakoid / protein-lysine N-methyltransferase activity / biosynthetic process / superoxide dismutase / superoxide dismutase activity / protein-disulfide reductase activity / response to light stimulus / : / DNA-directed RNA polymerase complex / cell redox homeostasis / chloroplast / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / kinase activity / regulation of cell shape / methylation / protein dimerization activity / cell division / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / Protein plastid transcriptionally active 7 / PLASTID TRANSCRIPTIONALLY ACTIVE protein 6 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Thioredoxin-like protein CITRX, chloroplastic / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / : / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' ...Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / Protein plastid transcriptionally active 7 / PLASTID TRANSCRIPTIONALLY ACTIVE protein 6 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Thioredoxin-like protein CITRX, chloroplastic / (S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / : / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / MurE/MurF, N-terminal / : / SAP domain superfamily / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / Thioredoxin / SET domain / SET domain superfamily / SET domain profile. / SET domain / S1 domain profile. / RmlC-like cupin domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Thioredoxin domain profile. / S1 domain / Thioredoxin domain / RmlC-like jelly roll fold / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7 / Uncharacterized protein LOC110792506 isoform X1 / superoxide dismutase / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2 / Uncharacterized protein LOC110798943 / Thioredoxin-like protein CITRX, chloroplastic / Fructokinase-like 1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Uncharacterized protein LOC110782000 / superoxide dismutase ...Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7 / Uncharacterized protein LOC110792506 isoform X1 / superoxide dismutase / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2 / Uncharacterized protein LOC110798943 / Thioredoxin-like protein CITRX, chloroplastic / Fructokinase-like 1, chloroplastic / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / Uncharacterized protein LOC110782000 / superoxide dismutase / Uncharacterized protein LOC110791626 / Fructokinase-like 2, chloroplastic isoform X2 / Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta'' / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWang G-L / Yu L-J / Lu C
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)2020YFA0907600 China
National Natural Science Foundation of China (NSFC)32000444 China
CitationJournal: Nat Commun / Year: 2024
Title: Architecture of the spinach plastid-encoded RNA polymerase.
Authors: Tongtong Wang / Guang-Lei Wang / Ying Fang / Yi Zhang / Wenxin Peng / Yue Zhou / Aihong Zhang / Long-Jiang Yu / Congming Lu /
Abstract: The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts, transcribing over 80% of all primary plastid transcripts. This polymerase consists of a ...The plastid-encoded RNA polymerase serves as the principal transcription machinery within chloroplasts, transcribing over 80% of all primary plastid transcripts. This polymerase consists of a prokaryotic-like core enzyme known as the plastid-encoded RNA polymerase core, and is supplemented by newly evolved associated proteins known as PAPs. However, the architecture of the plastid-encoded RNA polymerase and the possible functions of PAPs remain unknown. Here, we present the cryo-electron microscopy structure of a 19-subunit plastid-encoded RNA polymerase complex derived from spinach (Spinacia oleracea). The structure shows that the plastid-encoded RNA polymerase core resembles bacterial RNA polymerase. Twelve PAPs and two additional proteins (FLN2 and pTAC18) bind at the periphery of the plastid-encoded RNA polymerase core, forming extensive interactions that may facilitate complex assembly and stability. PAPs may also protect the complex against oxidative damage and has potential functions in transcriptional regulation. This research offers a structural basis for future investigations into the functions and regulatory mechanisms governing the transcription of plastid genes.
History
DepositionJan 21, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38799.png

Downloads & links

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Map

FileDownload / File: emd_38799.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å		1.1 Å/pix.
x 512 pix.
= 563.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.0508178 - 1.6966358
Average (Standard dev.)-0.0002616613 (±0.04288872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38799_half_map_1.map
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Half map: #1

Fileemd_38799_half_map_2.map
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Sample components

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Entire : spinach plastid-encoded RNA polymerase

EntireName: spinach plastid-encoded RNA polymerase
Components
  • Complex: spinach plastid-encoded RNA polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit beta''
    • Protein or peptide: Fructokinase-like 1, chloroplastic
    • Protein or peptide: Thioredoxin-like protein CITRX, chloroplastic
    • Protein or peptide: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12
    • Protein or peptide: pTAC3
    • Protein or peptide: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2
    • Protein or peptide: MurE
    • Protein or peptide: pTAC6
    • Protein or peptide: superoxide dismutase
    • Protein or peptide: superoxide dismutase
    • Protein or peptide: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10
    • Protein or peptide: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7
    • Protein or peptide: pTAC18
    • Protein or peptide: Fructokinase-like 2, chloroplastic isoform X2
  • Ligand: FE (III) ION

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Supramolecule #1: spinach plastid-encoded RNA polymerase

SupramoleculeName: spinach plastid-encoded RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9, #17, #10-#16
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 960 KDa

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Macromolecule #1: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 38.571656 KDa
SequenceString: MVREKIRVST QTLQWKCVES RTDSKCLHYG RFILSPLMKG QADTIGIAMR RALLGEIEGT CITRAKSEKI PHEYSTILGI QESVHEILM NLKEIVLRSN LYGTCEASIC VRGPRGVTAQ DIILPPYVEI VDNTQHIASL TEPIDLCIGL QLERNRGYHI K APNNFQDG ...String:
MVREKIRVST QTLQWKCVES RTDSKCLHYG RFILSPLMKG QADTIGIAMR RALLGEIEGT CITRAKSEKI PHEYSTILGI QESVHEILM NLKEIVLRSN LYGTCEASIC VRGPRGVTAQ DIILPPYVEI VDNTQHIASL TEPIDLCIGL QLERNRGYHI K APNNFQDG SFPIDALFMP VRNVNHSIHS YGNGNEKQEI LFLEIWTNGS LTPKEALYEA SRNLIDLLIP FLHAEENVNL ED NQHKVSL PLFTFHNRLA EIRKNKKKIA LKFIFIDQLE LPPRIYNCLK KSNIHTLLDL LNNSQEDLIK MKHFRIEDVK QIF GTLEKH FVIDLKNKR

UniProtKB: DNA-directed RNA polymerase subunit alpha

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Macromolecule #2: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 121.050531 KDa
SequenceString: MLRDGNEGMS TIPGFNQIQF EGFWRFIDQG LTEELSKFPK MEDTDQEIEF QLFVETYQLA EPLIKEKDAV YESLTYSSEL YVSAGLIWK TRREMQEQTI LIGNIPLMNS LGTFIVNGIY RIVINQILQS PGIYYRSELD HNGISVYTGT IISDWGGRSE L EIDRKARI ...String:
MLRDGNEGMS TIPGFNQIQF EGFWRFIDQG LTEELSKFPK MEDTDQEIEF QLFVETYQLA EPLIKEKDAV YESLTYSSEL YVSAGLIWK TRREMQEQTI LIGNIPLMNS LGTFIVNGIY RIVINQILQS PGIYYRSELD HNGISVYTGT IISDWGGRSE L EIDRKARI WARVSRKQKI SILVLSSAMG SNLREILDNV CYPEIFLSFL NDKEKKKIGS KENAILEFYQ QFACVGGDPV FS ESLCKDL QKKFFQQRCE LGRIGRRNMN RRLNLDIPEN NTFLLPRDIL AAADHLIGMK FGMGTLDDMN HLKHKRIRSV ADL LQDQFG LALVRLENVV RGTISGAIRH KLIPTPQNLV TSTPLTTTFE SFFGLHPLSQ VLDRTNPLTQ IVHGRKLSYL GPGG LTGRT ASFRIRDIHP SHYGRICPID TSEGINVGLI GSLAIHARIG PWGSLESPYY EISERSKRVQ MLYLSPSRDE YYMLA SGNS LALNQGIQEE QVVPARYRQE FLTIAWEQVH FRSIFSFQYF SIGASLIPFI EHNDANRALM SSNMQRQAVP LSQSEK CIV GTGLERQVAL DSGVLAIAEH EGKIIYTNTD KIVLLGNGNT VSIPLVMYQR SNKNTCMHQK PQIPRGKCVK KGQILAD GA ATVGGELALG KNVLVAYMPW EGYNFEDAVL ISERLVYEDI YTSFHIRKYE IQTYVTSQGP EKVTSEIPHL EAHLLRNL D KNGIVRLGSW VETGDILVGK LTPQMAKESS YAPEDRLLRA ILGIQVSTSK ETCLKLPIGG RGRVIDVRWI QKKGGSSYN PETIHVYISQ KREIKVGDKV AGRHGNKGII SRILLRQDMP YLQDGRPVDM IFNPLGVPSR MNVGQIFECS LGLAGSLLDR HYRIAPFDE RYEQEASRKL VFSELYEASK QTANPWVFEP EYPGKSRIFD GRTGDPFEQP VIIGNPYILK LIHQVDDKIH G RSSGHYAL VTQQPLRGRA KQGGQRVGEM EVWALEGFGV AHILQEMLTY KSDHIKARQE VLGTTIIGGT IPNPEDAPES FR LLVRELR SLALELNHFL VSERNFQINR MEA

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 78.257242 KDa
SequenceString: MIDQYKHQQL RIGSVSPQQI SAWATKILPN GEIVGEVTKP YTFHYKTNKP EKDGLFCERI FGPIKSGICA CGNYRVIGDE KEDPKFCEQ CGVEFVDSRI RRYQMGYIKL ACPVTHVWYL KRLPSYIANF LDKPLKELEG LVYCDFSFAR PIAKKPTFLR L RGLFEYEI ...String:
MIDQYKHQQL RIGSVSPQQI SAWATKILPN GEIVGEVTKP YTFHYKTNKP EKDGLFCERI FGPIKSGICA CGNYRVIGDE KEDPKFCEQ CGVEFVDSRI RRYQMGYIKL ACPVTHVWYL KRLPSYIANF LDKPLKELEG LVYCDFSFAR PIAKKPTFLR L RGLFEYEI QSWKYSIPLF FTTQGFDTFR NREISTGAGA IREQLADLDL RTIIDYSFAE WKELGEEGST GNEWEDRKVG RR KDFLVRR MELVKHFIRT NIEPEWMVLC LLPVLPPELR PIIQIDGGKL MSSDINELYR RVIYRNNTLT DLLSTSRSTP GEL VMCQEK LVQEAVDTLL DNGIRGQPMR DGHNKVYKSF SDVIEGKEGR FRETLLGKRV DYSGRSVIVV GPSLSLHRCG LPRE IAIEL FQTFVIRGLI RQHLASNIGV AKRKIREKEP IVWKILQEVM QGHPVLLNRA PTLHRLGIQA FQPILVEGRA ICLHP LVCK GFNADFDGDQ MAVHVPLSLE AQAEARLLMF SHMNLLSPAI GDPISVPTQD MLIGLYILTS GNRRGICANR YNPWNH KTY QNERIDDTNY KSMKEPFFCN FYDAIGAYRQ KRIHLDSPLW LRWQLDQRII ASKEAPIEVH YESLGTYHEI YAHYLII RS VKKEIIDIYI RTTVGHISLY REIEEAIQGF YQACS

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: DNA-directed RNA polymerase subunit beta''

MacromoleculeName: DNA-directed RNA polymerase subunit beta'' / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 154.507516 KDa
SequenceString: MAERANLVFH NKAIDGTAMK RLISRLIDHF GMAYTSHILD QLKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYSTSE YLRQEMNPNF RMTDPYNPVH IMSFSGARGN VSQVHQLVGM RGLMSDPQGQ M IDLPIQSN ...String:
MAERANLVFH NKAIDGTAMK RLISRLIDHF GMAYTSHILD QLKTLGFQQA TATSISLGID DLLTIPSKGW LVQDAEQQSL ILEKHHHYG NVHAVEKLRQ SIEIWYSTSE YLRQEMNPNF RMTDPYNPVH IMSFSGARGN VSQVHQLVGM RGLMSDPQGQ M IDLPIQSN LREGLSLTEY IISCYGARKG VVDTAVRTSD AGYLTRRLVE VVQHIVVRRR DCGTIRGISV SPQNSTMPER IL IQTLIGR VLADDIYMGS RCIATRNQDI GVGLVNRFIT LRTQLISIRT PFTCRSASWI CRLCYGRSPT HGGLVELGEA VGI IAGQSI GEPGTQLTLR TFHTGGVFTG GTAEHVRAPS NGKIQFNEDL VHPTRTRHGH PAFLCYIDLY VTIESDDILH NVNI PPKSF LLVQNDQYVE SEQVIAEIRA GTSTLNFKER VRKHIYSDSE GEMHWSTDVY HAPEFTYGNV HLLPKTSHLW VLSGK PYRS SVVPFSLSKD QDQMNTHSLS FEQIYISNPS VTNDQVKDKL SDSFSKKEDR ITDYSELNRI GHCNLIYPAK NLDLLA KKR RNRFIIPFQG SQERKKELMS LSGISIEIPI NGIFRKNSIF AYFDDPRYRR KSSGITKYGT IEMHSIVKKE DLIEYRG VK EFRPKYQMKV DRFFFIPEEV HILAGSSSIM VRNNSIIGVD TWITLNTRSR IGGVVRVERK KKKIELTIFS GDIHFPGE T DKISRHSGIL IPPSRKNSKD SKNLKKWIYV QRITPTKKKY FVLVRPVVPY EITDGINLAT LFPQDLLQER DNVQLRVVN YILYGNGKVT RGISDTSIQL VRTCLVLNWN QDKKGSSIEE ARGSFVEVRT NGMIQDFLKV NLVKPAISYI SKRNDPSSEK KEGSDHTNM NPFYSIYIYP KTKLQKSFNQ NQGTVRTLLG INKECQFFLI LSSSNCFRIG PFKGVKYPKE LIKKDPLIPI R NSFGPLGT ALQIANFFSF YYLITHNQIL VTNYLQLDNL KQTFQPFKFQ YYLMDENGRI YNPDPCSNII FNPFKLNWYF LH YHFCEET STKIDLGQFV CENVCITKKG THLKSGQVLI VQFDSVVIRS AKPYLATPGA TLHGHYGEII YEGDTLVTFI YEK SRSGDI TQGLPKVEQV LEVRSIDSIS INLEKRIDSW NERITRILGS PWGFLIGAEL TIAQSRISLV NKIQKVYRSQ GVQI HNRHI EIIVRQITSK VLVSEDGMSN VFLPGELIGL FRAERTGRAL EEAICYRATL LGITRASLNT QSFISEASFQ ETARV LAKA ALRGRIDWLK GLKENVVLGG MIPVGTGFKG FVHHSSQHKD IPLKTKKQNL FEGEMGDILF YHRELFESCL SKN

UniProtKB: DNA-directed RNA polymerase subunit beta''

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Macromolecule #5: Fructokinase-like 1, chloroplastic

MacromoleculeName: Fructokinase-like 1, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 53.566363 KDa
SequenceString: MAIHILSPIP SSLFLSPIPT PLFPPFSTST QIRASTNSNN GVQEPPKRRG RPKGSTKSNT PKTPKKLSGS SQNAEFENGS TLTWDELED FDDGMDFPYL DPPLICCFGA VQKEFVPSVR VSEHQMDPDI YSGWKMMQWN PPEFGRAPGG PVSNVAISHV R LGGRAAVI ...String:
MAIHILSPIP SSLFLSPIPT PLFPPFSTST QIRASTNSNN GVQEPPKRRG RPKGSTKSNT PKTPKKLSGS SQNAEFENGS TLTWDELED FDDGMDFPYL DPPLICCFGA VQKEFVPSVR VSEHQMDPDI YSGWKMMQWN PPEFGRAPGG PVSNVAISHV R LGGRAAVI GKVGEDDFGE ELVLMMNKEN VQTRAVKFDS NVKTACSYMR VKFSDDGKMK METVKEAAED SLVASELNLA VL KEARIFH FNSEVLTSPS MNTTLFRAIK LSKKFGGLVF FDLNLPLPLW KSRDETREVI KQAWEEANII EVSREELEFL LDE DHYERR KNYRPQYYSE NYEQSKNRRD YYHYTREEIS PLWHDGLKFL FVTDGTLRIH YYAPSFDGVV VGTEDVLITP FTCD RTGSG DAVVAGIMRK LTSHPEMYED QDVLERQLRF SIAAGIISQW TIGAVRGFPT ESATQNLKEQ VYVPSMW

UniProtKB: Fructokinase-like 1, chloroplastic

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Macromolecule #6: Thioredoxin-like protein CITRX, chloroplastic

MacromoleculeName: Thioredoxin-like protein CITRX, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 20.586947 KDa
SequenceString:
MQIPTAPRSI SSAASNLFLY FPPFHLNSSL IKPTTLNFPL NHNLPTSISI PTLIPTKKLL CKPPSAKHVR EDYLVKKLSA NEITELVRG ERNVPLIIDF YATWCGPCIL MAQELEMLAV EYEKNAMIVK VDTDDEYEFA RDMQVRGLPT LYFISPDPNK D AIRTEGLI PIQMMRDILD NDM

UniProtKB: Thioredoxin-like protein CITRX, chloroplastic

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Macromolecule #7: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12

MacromoleculeName: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 59.779086 KDa
SequenceString: MANLSTNWVF QDRGLRCMIP CDGSFFKASS SNSMLLNRGR LCPLPARSRL HSIKCQQEEE AFEEVSVERA PYYSYKDSSS GRIEPASGA RASIPGQDYW PEGTADRVRA ARAPEPKGES TSDSSFGKRP GSRRKNYKGS VAVAVAGSQE LSPVLSDPEL T ETSDDIGE ...String:
MANLSTNWVF QDRGLRCMIP CDGSFFKASS SNSMLLNRGR LCPLPARSRL HSIKCQQEEE AFEEVSVERA PYYSYKDSSS GRIEPASGA RASIPGQDYW PEGTADRVRA ARAPEPKGES TSDSSFGKRP GSRRKNYKGS VAVAVAGSQE LSPVLSDPEL T ETSDDIGE DPIDSSEYVV YQADLESEEL SEYEKDKKFG RPHPFVDPKV KKPIEEPLTS EELWWNWRKP DKEQWSRWQR RK PDVETVF LKAMAETGQV KLYGEQPTLT ETSLYRARRH LFKEERLKAE QERLEKIGPM AFYSEWVKAW KGDTSREAIQ KHF EETGED ENTQLIEMLS HQTDREYRIM MGTDIRIRRD PLAMRMREDQ IKEIWGGDPV YPTINYIQDP DIVIDYRGPD FHEP TPNML AHLKEHGKII SREDLEKLLA KEKTEEHELA EVDDAMARAI DIGENEDEDE DSDSEGNDEA EEKINRNWSV HKSNP QLRK SKDKPKKKDS LSLDEAVDDS ENLTDFLLDF DEED

UniProtKB: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 12

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Macromolecule #8: pTAC3

MacromoleculeName: pTAC3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 101.669648 KDa
SequenceString: MAHILSSKFL PFNPTLHPSP HFLSPPPLKP PNSVIVSAVS TTERKSRRRR QPKGDDTSVA GSSAAEKGLR LVFMEELMSK ARNRDAIGV SDVIYDMIVA GLTPGPRSYH GLVVAHVLNA DEEGAMKSLR RELSVGLVPL HETFVALVRL FGSKGRATRG L EILAAMEK ...String:
MAHILSSKFL PFNPTLHPSP HFLSPPPLKP PNSVIVSAVS TTERKSRRRR QPKGDDTSVA GSSAAEKGLR LVFMEELMSK ARNRDAIGV SDVIYDMIVA GLTPGPRSYH GLVVAHVLNA DEEGAMKSLR RELSVGLVPL HETFVALVRL FGSKGRATRG L EILAAMEK LNYDIRKAWL VLVEELVRSN HLEDANKVFL KGAKGGLRAT DEIYDLMIEE DCKSGDHSNA LTIAYEMEAA GR MATTFHF NCLLSVQANC GIPEVAFATF ENMEFGEDYM KPDTETYNWV IQAYTRAESY DRVQDVAELL GLMVEDHKRL QPN MRTHVL LVECFTKYCV IREAIRHFRA LKNFEGGTRL LHSQGNFGDP LSLYLRALCR EGRIEELLDA LETMAKDNQP IPPR AMILS RKYRTLISSW IEPLQEEAEL GYEVDYMARY ISEGGLTGER KRWVPRRGKT PLDPDVEGFI YSNPVETSFK QRCLE EWKI RHRKLLRHLR NEGPAVLGAN ASESDYIRVE ERLKKIIKGR EKNILKPKAA SKMVVSELKE ELEAQDLPID GTRNVL YQR VQKARRINIS RGRPLWVPPV LEEEEEVDEE LDELISRIKL EEGNTEFWKR RFLGERVIYD NMKPMDGQES EPEETMD DA DIVDDGTKEV EEDEADDEEE EAEVEVEVEQ TEGQEDLVDR VKDKEVEAKK PLQMIGVQLL KDGDQPTTSK KSRRRARR A AENDDDDDWF PLDLYEAFEE MRKRNIFDVE NMYTLADAWG WTWERELKNR PPRRWSQEWE VELAIKIMSK VIELGGIPT IGDCAIILRA AIKAPLPSAF LIILQTTHSL GYRFGSPLYD EIITLCLDLG ELDAAVAIVA DLETSGITVP DETLDKVIAA RQIFDSPAD EAS

UniProtKB: Uncharacterized protein LOC110792506 isoform X1

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Macromolecule #9: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2

MacromoleculeName: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 56.522461 KDa
SequenceString: MTSHSISMAS TILLHHSPHR FLSNFQLCSF NNGFPTARKP NSTVSTSENT LRPVKSLVET SSFPLFQEPQ IVETTSEMNL ADPDFYKIG YVRSFRAYGV EFREGPDGFG VFASKDIEPL RRARMIMEIP LELMLTISKR LPWMFFPDIV PVGHPIFDII N STDPKTDW ...String:
MTSHSISMAS TILLHHSPHR FLSNFQLCSF NNGFPTARKP NSTVSTSENT LRPVKSLVET SSFPLFQEPQ IVETTSEMNL ADPDFYKIG YVRSFRAYGV EFREGPDGFG VFASKDIEPL RRARMIMEIP LELMLTISKR LPWMFFPDIV PVGHPIFDII N STDPKTDW DLRLACLLLL AFDQEDNFWQ LYGDFLPSAD ECTSLLLATE EDLLELQDES LELTMREQQH RCLEFWEKNW HS AAPLKIK RLARDPKIFM WAASIAQTRC INMEMRIGAL IQDANVLVPY ADMLNHSFQP NCFFHWRFKD RMLEVMINPG SRI KKGEEM TVNYLSGQQN NIFMQRFGFS SAVNPWDAIC FSGDSRIHLD TFLSVFNITG LRQEYYYNSK SAKEGDSFVD GAVI AAART LPTWSDRDVP IIPSVERKAA KELQEQCHEI LAKYPTTAKQ DQQILDATED GRRTLEAAIK YRLHRKLFIG KVIDA LEIY QDRILF

UniProtKB: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 14 isoform X2

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Macromolecule #10: pTAC6

MacromoleculeName: pTAC6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 37.791477 KDa
SequenceString: MTSTFLLLPT QLLPPKPPFL PFCTLSPPPT TTTTLSLLRP PPLFTSLKSR DFRVFSDDGD GDGEYEMDDE EAEEVDNKKD FDVEYEPLG VVSSAGMSAD EVIQVIQSKN FVSTQGWNSE LVVDYRINED EFHKICLFDC DFFIRKPPDP DNDVYDFREM Y VTPPDTDV ...String:
MTSTFLLLPT QLLPPKPPFL PFCTLSPPPT TTTTLSLLRP PPLFTSLKSR DFRVFSDDGD GDGEYEMDDE EAEEVDNKKD FDVEYEPLG VVSSAGMSAD EVIQVIQSKN FVSTQGWNSE LVVDYRINED EFHKICLFDC DFFIRKPPDP DNDVYDFREM Y VTPPDTDV YAIPKVLAPM PDKYIRCAKT DYGWYNVTEP PIDAPRDPMY KSEREVSKVF LTKHYRNRRL NDPEFVLDFE EI YVIDSRT KSVTRARVLV TVPEGRNRDR KGDLLVIRDN GNSFKITHAS KRDDPTTVIE REEWTRTRQD MERHLRKLRD FSI SNWI

UniProtKB: Uncharacterized protein LOC110782000

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Macromolecule #11: superoxide dismutase

MacromoleculeName: superoxide dismutase / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 31.983906 KDa
SequenceString: MSAVAAPSAI SISSSFLTHP VMFAGFKGGL NSTRFSPWKL KETRVRRASA DVVTAKFDLN PPPYPIDALE PHMSKQTFEY HWGKHHRAY VDNLNKQIVG TELDGLPLEE VVRITYNKGD MLPAFNNAAQ AWNHEFFWES MKPGGGGKPS GELLAQIEKD F GSFEAFTT ...String:
MSAVAAPSAI SISSSFLTHP VMFAGFKGGL NSTRFSPWKL KETRVRRASA DVVTAKFDLN PPPYPIDALE PHMSKQTFEY HWGKHHRAY VDNLNKQIVG TELDGLPLEE VVRITYNKGD MLPAFNNAAQ AWNHEFFWES MKPGGGGKPS GELLAQIEKD F GSFEAFTT EFKTAAATQF GSGWAWLVYK ANKLDVGNAV NPKPSEDDKK LVVVKSPNAV NPLVWDYYPI LTVDVWEHAY YL DFQNRRP DYLSIFMENL VSWDAVNARY EAAKAFATER EEEAAQN

UniProtKB: superoxide dismutase

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Macromolecule #12: superoxide dismutase

MacromoleculeName: superoxide dismutase / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 31.092381 KDa
SequenceString: MLLTSKGVGK SEMGSLTATN PVSSPLHANG LSSRIKCPTF FNQKRRDEGS KRRPGVVAYY GLKKPPYNLD ALEPYMSQKT LESHWGVQH RNYLEALNRH LSRSDTLYGH TMDELVKVTY NYGNPLPEFN DAAQVWNHDF FWESMQPGGG ESPTLGLLQQ I EKDFGSFP ...String:
MLLTSKGVGK SEMGSLTATN PVSSPLHANG LSSRIKCPTF FNQKRRDEGS KRRPGVVAYY GLKKPPYNLD ALEPYMSQKT LESHWGVQH RNYLEALNRH LSRSDTLYGH TMDELVKVTY NYGNPLPEFN DAAQVWNHDF FWESMQPGGG ESPTLGLLQQ I EKDFGSFP NFKEKFIEAA MTLFGSGWVW LVLKRKEKQL AVVKTSNAVT PILWDDIPII CLDLWEHAYY LDYKNDRAEY VN VFMNHLV SWHAATARLA RAQAFVNLGE PKIPVA

UniProtKB: superoxide dismutase

+
Macromolecule #13: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10

MacromoleculeName: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 80.48282 KDa
SequenceString: MQILQTSHFL PLSLLPKTPL KPPIPIFHNP NFHPNFSLLS SSSSLLPIPP KSYASDEFPV DETFLEQFGP KDTETEEEAR KRNWVERGW APWEEILSPE ADFARKSLNE GEEVALKNPD TIEAFKMLKP SYRKKKMEEM GLTEDEYYAR QFDIKGEILD P LETYWDGP ...String:
MQILQTSHFL PLSLLPKTPL KPPIPIFHNP NFHPNFSLLS SSSSLLPIPP KSYASDEFPV DETFLEQFGP KDTETEEEAR KRNWVERGW APWEEILSPE ADFARKSLNE GEEVALKNPD TIEAFKMLKP SYRKKKMEEM GLTEDEYYAR QFDIKGEILD P LETYWDGP LVVRHVAPRD WPPPGWEVDR KELEFIREGH KMMAERVDMK ELDNVIREKE GMCMDRYKVF LKQYQEWVEF NK DKLEEES YEHDQDYHPG RRKRGKDYEE GMYELPFYYP GQICLGKVTT LHLYQGAFVD VGGVYEGWVP IKGNDWYWIR QHI KVGMHV MVEILAKRDP YRFRFPLELR FVDPNIDHLL FQRFEYPPIF HRDEDTNLDE LRRDCRRPPF PRKDPGVKVE EEPL LSDHP YVDKLWQINV AEQMILDDME ANPDKYKGKK LSELTDEEEF DEEHSVEYTK VQYKKSLLPK TILKTSVKEL DLESA FAER QLHNRLQKEA EERGEDYKVD KLRRNIEMDE YDFIHWRRSF EEREALLRDI SCRQALGLPL QEPGRYVDPS ILGKDQ YDP SHPLYRYDYW GEPKNSEKTK QERVTDAHNK SVVGKGNVWY EMSYEDAVEE MKYRESHPKD NTERETDEEA ESDDDDS DD DFDYSILSDL SADFASQPHV NGTESPSISD EGMFEE

UniProtKB: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10

+
Macromolecule #14: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7

MacromoleculeName: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 19.339039 KDa
SequenceString:
MSLSLSSLPF NSLLPLSSST KFEAGPIILR PLGFSIRSQA KPKSRSPVQN GRQVWRRRKL SKKDVFMEAK LERVPFLEEQ MRKVNEGGG VMAGDIDRLM KSEDNRFAFV NEIAAEATAY VNNNRDEYGH KKAIHHVLSN RMNDAGFARP EAYLETEPFS P GPTYLKEN FY

UniProtKB: Protein PLASTID TRANSCRIPTIONALLY ACTIVE 7

+
Macromolecule #15: pTAC18

MacromoleculeName: pTAC18 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 17.109521 KDa
SequenceString:
MASVIWSPTF HSSVIRTNKS ELKRCDHNVS RSGCIKAMRI EKPLEELYKI RVERKVSPER LNELGVSRWT TWKTGKCRLP WDWHVDQLV YIEEGEVRVV PEGSKHYMSF KAGDLVRYPK WFEADLWFNA FYQERYSFRA YGDD

UniProtKB: Uncharacterized protein LOC110798943

+
Macromolecule #16: Fructokinase-like 2, chloroplastic isoform X2

MacromoleculeName: Fructokinase-like 2, chloroplastic isoform X2 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 65.597586 KDa
SequenceString: MASLSFTQFR SIPRWNYKAP VLATVEFMLV TDHRLQNRCV LSETSKKAIV ASVVQDEGPN EPEGTKKTRT RRTTTRGRKK ATTELQDGD SELTLSASAS EQEISDPEAS ISGSEKPKRR TRKKVLHTEM KLFSAVSAIS TEKVKTEKKP RGRKRKEETS K VDDDISET ...String:
MASLSFTQFR SIPRWNYKAP VLATVEFMLV TDHRLQNRCV LSETSKKAIV ASVVQDEGPN EPEGTKKTRT RRTTTRGRKK ATTELQDGD SELTLSASAS EQEISDPEAS ISGSEKPKRR TRKKVLHTEM KLFSAVSAIS TEKVKTEKKP RGRKRKEETS K VDDDISET EFINLEEVVY LADEENEDDN IDLNLEKCNG EDIDFTYGWP PLVCCFGAAQ HAFVPSGRPA NRLIDHQIHE AL KEALWAP DKFIRAPGGS AGGVAIALAS LGGRVAFMGK LGNDDYGQTM LYYLNVKSVQ TRSVCVDDKR WTAMSQMKIA KRG ALRATT VKPCAEDSLS KSEINIDVLK EAKMFYLNTS SLVDANMRKT TMRALKISKK LGSVIFYDLN LPLPLWKSGE ETKS LIQQV WSLADVIEVT KQELEFLCGM NPPEEFDTKK NQRFKFEHYE ADIIAPLWHE NLKVLFVTNG TSKIHYYTKE HNGAV LGVE DAPMSPFTQD MSASGDGLVA ALMRMLAVQP HLITDKEYLE RSVKYAINCG VIEQWIVTRQ QGYPPKVGIE EDEEET IPD PSGIRSTTER EFRTRMPVLC

UniProtKB: Fructokinase-like 2, chloroplastic isoform X2

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Macromolecule #17: MurE

MacromoleculeName: MurE / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 85.420578 KDa
SequenceString: MFLQPFLTLP STISSPTNSS SSSSSLHFTK PLFLRPSISL LRRKTPSAAG NYYPNPSDDD PPEAPEDSSH GVSKFGQIQR QAARARKLE EEDFEKNRSV FLDAIKDVED APENEDYSTG VSGSGDDLFG DIDKAIAQKR KEFVKKGLLK PNPPKSERVV E VADDELGQ ...String:
MFLQPFLTLP STISSPTNSS SSSSSLHFTK PLFLRPSISL LRRKTPSAAG NYYPNPSDDD PPEAPEDSSH GVSKFGQIQR QAARARKLE EEDFEKNRSV FLDAIKDVED APENEDYSTG VSGSGDDLFG DIDKAIAQKR KEFVKKGLLK PNPPKSERVV E VADDELGQ EEVVDLEEID ELQGLRVVDV SEKEEEFDDD DIDVEVSELG KNGSSSSLFD ASFDIDFDSL GNNSSNKVRI VE PSFKMTL AELLDECKVV PISVYGDLEV EITGIEHDSR LVNSGDLFVC CVDGNLCLIE ADKRGAVAVV ASKEIDIEET LGC KALVIV EDTNAALPAL AAAFFRYPTK SMSVIGITGT HGKTTAAHLI KTMYEAMGLR TGMMSSVAYY VHGDNKLDFP EANP DAVLV QKLMAKMLHN GTEAVVMEAS SNELTHTRCE EIDFDIAVFT NLSRDNSHFQ GNEEEFRVAQ AKLFSRMVDP DRHRK IVNV DDPNAPFFIA QGNPNVPVLT FALENKDADV HPLKFELSLF ETTVLVNTPQ GILEISSGLL GRHNIYNILA AVTVGI AVG APLEDIVRGI EEVDAVPGRC EVIDEEQAFG VIVDHARTPD ALSRLLDSVR ELQPRRIITV IGSCGEKERG KRPMLAK VA TDKSDVTMLT SDNQGSEDPL DILDDMLAGI GWTMQDYLKH GENDYYPPLP NGHRLFLHDI RRVAVRCAVA MGEEGDMV V VAGKGHEAYQ VDGDKKEFFD DREECREALQ YVDELHQAGI DTSEFPWRLP ESH

UniProtKB: Uncharacterized protein LOC110791626

+
Macromolecule #18: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 18 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8zgz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180924
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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