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- EMDB-34397: Cryo-EM structure of Synechocystis sp. PCC 6803 RPitc -

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Basic information

Entry
Database: EMDB / ID: EMD-34397
TitleCryo-EM structure of Synechocystis sp. PCC 6803 RPitc
Map data
Sample
  • Complex: The complex of Synechocystis sp. PCC 6803 RPitc
    • Protein or peptide: x 6 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 2 types
KeywordsCryo-EM / Synechocystis sp. PCC 6803 / Syn6803 / Transcription initiation / RPitc / Transcription / Cyanobacteria / TRANSCRIPTION-DNA-RNA complex
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase sigma factor, RpoD-like, cyanobacteria / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 ...RNA polymerase sigma factor, RpoD-like, cyanobacteria / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / 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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like 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 3 / RNA polymerase Rpb1, domain 3 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit gamma / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsShen LQ / You LL / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: An SI3-σ arch stabilizes cyanobacteria transcription initiation complex.
Authors: Liqiang Shen / Giorgio Lai / Linlin You / Jing Shi / Xiaoxian Wu / Maria Puiu / Zhanxi Gu / Yu Feng / Yulia Yuzenkova / Yu Zhang /
Abstract: Multisubunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all ...Multisubunit RNA polymerases (RNAPs) associate with initiation factors (σ in bacteria) to start transcription. The σ factors are responsible for recognizing and unwinding promoter DNA in all bacterial RNAPs. Here, we report two cryo-EM structures of cyanobacterial transcription initiation complexes at near-atomic resolutions. The structures show that cyanobacterial RNAP forms an "SI3-σ" arch interaction between domain 2 of σ (σ) and sequence insertion 3 (SI3) in the mobile catalytic domain Trigger Loop (TL). The "SI3-σ" arch facilitates transcription initiation from promoters of different classes through sealing the main cleft and thereby stabilizing the RNAP-promoter DNA open complex. Disruption of the "SI3-σ" arch disturbs cyanobacteria growth and stress response. Our study reports the structure of cyanobacterial RNAP and a unique mechanism for its transcription initiation. Our data suggest functional plasticity of SI3 and provide the foundation for further research into cyanobacterial and chloroplast transcription.
History
DepositionSep 27, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34397.png

Downloads & links

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Map

FileDownload / File: emd_34397.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0106
Minimum - Maximum-0.09907036 - 0.14062358
Average (Standard dev.)0.00021672047 (±0.003545578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34397_msk_1.map
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Additional map: #1

Fileemd_34397_additional_1.map
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Half map: #2

Fileemd_34397_half_map_1.map
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Half map: #1

Fileemd_34397_half_map_2.map
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Sample components

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Entire : The complex of Synechocystis sp. PCC 6803 RPitc

EntireName: The complex of Synechocystis sp. PCC 6803 RPitc
Components
  • Complex: The complex of Synechocystis sp. PCC 6803 RPitc
    • 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 gamma
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • DNA: Nontemplate strand DNA
    • DNA: Template strand DNA
    • RNA: RNA (5'-R(*UP*CP*GP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: The complex of Synechocystis sp. PCC 6803 RPitc

SupramoleculeName: The complex of Synechocystis sp. PCC 6803 RPitc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 500 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: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 36.657344 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMAQFQI ECVESSTRKN QQQYSKFSLE PLDRGQGTTV GNALRRVLLS NLPGAAVTAI RIAGVNHEFA TILGVREDV LEIMLNMKEL VLKSYTDQPQ IGRLTAIGPG TVTAAQFEVP SEVEVIDPNQ YIATLAEGAK LEMEFRVERG V GYRVIERG ...String:
MGSSHHHHHH SQDPMAQFQI ECVESSTRKN QQQYSKFSLE PLDRGQGTTV GNALRRVLLS NLPGAAVTAI RIAGVNHEFA TILGVREDV LEIMLNMKEL VLKSYTDQPQ IGRLTAIGPG TVTAAQFEVP SEVEVIDPNQ YIATLAEGAK LEMEFRVERG V GYRVIERG KDENSSLDFL QIDSVFMPVT KVNYTVEDIR ADGMSPKDRL ILDIWTNGSI QPREALSEAS DIIANLFIPL KD LNELEAA HSDYQDEVNP ESQIPIEELQ LSVRAYNCLK RAQINSVADL LEYSQEDLLE IKNFGLKSAE EVIEALQKRL GIT LPHEKA KA

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: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 123.719812 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMTNLATTM LPDLIEIQHA SFHWFLEEGL IEELNSFSPI SDYTGKLELH FLGKDYKLKQ PKYDVDESKR RDASYSVQMY VPTRLINKE TGEIKEQEVF IGDLPLMTER GTFIINGAER VIVNQIVRSP GVYYKKELDK NGRRTYSASL IPNRGAWLKF E TDKNGLVY ...String:
MAMTNLATTM LPDLIEIQHA SFHWFLEEGL IEELNSFSPI SDYTGKLELH FLGKDYKLKQ PKYDVDESKR RDASYSVQMY VPTRLINKE TGEIKEQEVF IGDLPLMTER GTFIINGAER VIVNQIVRSP GVYYKKELDK NGRRTYSASL IPNRGAWLKF E TDKNGLVY VRIDKTRKLS AQVLLKAIGL SDNEILDSLS HPEFYQKTLD KEGNPTEEEA LVELYKKLRP GEPPTVSGGQ QL LESRFFD PKRYDLGRVG RYKLNKKLRL NEADTTRVLT PQDILAAINY LINLEFDVGT TDDIDHLGNR RVRSVGELLQ NQI RVGLNR LERIIRERMT VSESDALTPA SLVNPKPLVA AIKEFFGSSQ LSQFMDQTNP LAELTHKRRI SALGPGGLTR ERAG FAVRD IHPSHHGRIC PVETPEGPNA GLIGSLATCA RVNDYGFIET PYFRVESGRV RKDLDPVYLT ADEEDDMRVA PGDIP TDEE GNIIGESVPI RYRQEFSTTS PEQVDYVAVS PVQIISVATS MIPFLEHDDA NRALMGSNMQ RQAVPLLRPE RPLVGT GLE AQAARDSGMV IVSRTHGIVT YVDATEIRVQ PHSPDNPAEK GEEIVYPIQK YQRSNQDTCL NQRPLVYAGE DVVPGQV LA DGSATEGGEL ALGQNILVAY MPWEGYNYED AILISERLVY DDVYTSIHIE KFEIEARQTK LGPEEITREI PNVGEDAL R NLDEHGIIRI GAWVESGDIL VGKVTPKGEA DQPPEEKLLR AIFGEKARDV RDNSLRVPNG EKGRVVDVRV FTREKGDEL PPGANMVVRI YVAQKRKIQV GDKMAGRHGN KGIISRILPI EDMPYLPDGR PIDIALNPLG VPSRMNVGQV FECLLGWAGE NLGVRFKIT PFDEMYGEEA SRDTVHGLLE EASQRPNKDW VFNENHPGKI QVFDGRTGEP FDRPITVGQA YMLKLVHLVD D KIHARSTG PYSLVTQQPL GGKAQQGGQR FGEMEVWALE AYGAAYILQE LLTVKSDDMQ GRNEALNAIV KGKSIPRPGT PE SFKVLMR ELQSLGLDIA AHKVQLSEDG ESADAEVDLM IDSQRRAPNR PTYESLHTEE DLEEEEV

UniProtKB: DNA-directed RNA polymerase subunit beta

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Macromolecule #3: DNA-directed RNA polymerase subunit gamma

MacromoleculeName: DNA-directed RNA polymerase subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 71.072992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKAQSEPRFD YVKIAIASPE RIRQWGERTL PNGTVVGEVT KPETINYRTL KPEMDGLFCE KIFGPSKDWE CWCGKYKRVR HRGIVCERC GVEVTESRVR RHRMGYIKLA APVTHVWYLK GIPSYLSILL DMALRDVEQI VYFNAYVVLN PGNASNLQYK Q LLTEDQWV ...String:
MKAQSEPRFD YVKIAIASPE RIRQWGERTL PNGTVVGEVT KPETINYRTL KPEMDGLFCE KIFGPSKDWE CWCGKYKRVR HRGIVCERC GVEVTESRVR RHRMGYIKLA APVTHVWYLK GIPSYLSILL DMALRDVEQI VYFNAYVVLN PGNASNLQYK Q LLTEDQWV EIEDQIYAED SELEGIEVGI GAEAVQRLLA ELQLEEVAEK LREEILASKG QKRAKLIKRL RVIDNFIATH SQ AEWMTLD VIPVIPPDLR PMVQLDGGRF ATSDLNDLYR RVINRNNRLA RLQEILAPEI IVRNEKRMLQ EAVDALIDNG RRG RTVVGA NNRALKSLSD IIEGKQGRFR QNLLGKRVDY SGRSVIVVGP NLKIYQCGLP REMAIELFQP FVIHRLIKLG IVNN IKAAK KLILKGDPQI WSVLEEVITG HPVMLNRAPT LHRLGIQAFE PILVEGRAIQ LHPLVCPAFN ADFDGDQMAV HVPLS LEAQ CEARLLMLAC HNVLSPATGK PIVAPSQDMV LGCYYLTAEN PNAQKGAGRY FAGIEDALRA YDHGQVDLHS QIWIRH LDE DVVTEKPDTE VIKTEDLGDG TVMKYYRERK IREGVDGEII TQYIQTTPGR IIYNKTIAEA LVF

UniProtKB: DNA-directed RNA polymerase subunit gamma

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Macromolecule #4: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 8.749776 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTKRSNLDSN HIIYRSEELL GAASNRYNIT VRVAKRAKEN RSEDFDSIDD PNMKPAIRAI IEMSDELTRP EIISDN

UniProtKB: DNA-directed RNA polymerase subunit omega

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Macromolecule #5: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 50.335371 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMGMTQTKE PLTKAESAEL EQEIELSQYI NTDDIDDDDI DVEDLEQEVA ATEGKEKKVR KIRKDAVKKK PYTEDSIRIY LQEIGRIRL LRAEEEIELA RQIADLLELE LIRDNLTLQL ERQPSELEWG KQVWKLETAK QRLVGDKKKE PKKKDIDSYL A NPDNELSL ...String:
GAMGMTQTKE PLTKAESAEL EQEIELSQYI NTDDIDDDDI DVEDLEQEVA ATEGKEKKVR KIRKDAVKKK PYTEDSIRIY LQEIGRIRL LRAEEEIELA RQIADLLELE LIRDNLTLQL ERQPSELEWG KQVWKLETAK QRLVGDKKKE PKKKDIDSYL A NPDNELSL ENEWSQQPNK NFAAFRRRLF LDRRAKDKMV QSNLRLVVSI AKKYMNRGLS FQDLIQEGSL GLIRAAEKFD HE KGYKFST YATWWIRQAI TRAIADQSRT IRLPVHLYET ISRIKKTTKL LSQEMRRKPT EEEIAEKMEM TIEKLRFIAK SAQ LPISLE TPIGKEEDSR LGDFIEADGE TPEDEVSKNL LREDLENVLD TLSPRERDVL RLRYGLDDGR MKTLEEIGQI FNVT RERIR QIEAKALRKL RHPNRNSILK EYIR

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 145.371984 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSGSGSMTFY NYTIDKGRLK KLIALAYRRY GSARCSQLAD ELKELGFRFA TKAGVSISVD DLTIPPEKKQ MLEAAEKEIR TTEERYARG EITEVERFQK VIDTWNGTSE ELKDQVVVNF RKTDPLNSVY MMAFSGARGN MSQVRQLVGM RGLMADPQGE I IDLPIKTN ...String:
GSGSGSMTFY NYTIDKGRLK KLIALAYRRY GSARCSQLAD ELKELGFRFA TKAGVSISVD DLTIPPEKKQ MLEAAEKEIR TTEERYARG EITEVERFQK VIDTWNGTSE ELKDQVVVNF RKTDPLNSVY MMAFSGARGN MSQVRQLVGM RGLMADPQGE I IDLPIKTN FREGLTVTEY VISSYGARKG LVDTALRTAD SGYLTRRLVD VSQDVIVREQ DCGTERSLRV TAMTDGDQVK IS LADRLFG RLLAKDVVGP DGEIIAKRND EIDEALANRI AAVTDEVYVR SPLTCEAARS VCQNCYGWSL AHGHKVDLGE AVG IIAAQS IGEPGTQLTM RTFHTGGVFT GEVARQEKAP EDGTVKWGKG LSTRKVRTRH GEDAEQVEIA GDLIWKGEGK KAAT QTYSL TPGSLLFVQD GQTVTAGQLM TEISLSKTQR STERATKDVA GDLAGEVLFD RLVPEEKTDR QGNTTRIAQR GGLVW ILSG EVYNLPPGAE PVVKNDEQVE VGSIMAETKL VTNDGGVVRL VSNREIEIIT ASVLLDQAQV KLESSGGREQ YVIYTA DKQ RFLLKAAPGT KVQNHSIVAE LIDDRYRTTT GGMIRYAGVE VAKGGRKQGY EVTKGGTLLW IPEETHEINK DISLLIV ED GQYVEAGTEV VKDIFCQSSG IVEVVQKNDI LREIIIKPGD FYQDVDPGSV KIESGQLLQP GQDVFPGVTV STLSQAEW I ESPEGNGLLL RPVEEYKVFD EPAAPSQGSQ NEEGGRQIEL RSVQRLFYKD GDRVKSVEGA PLLSTQLVLE IYGSGNEGI SHLSADIELQ DDEEEDCQRL QLVILESLVL RRDQESDPLG GASKTRLLVQ DGDQIPPGAV VARTEIQCKE AGTVRGIKEG QESIRRVLL ERAADRLVVD LPSAPEVKPG QLLVAGQELV PGVKLEESGK VLEINGKGDN YQLVLRRARP YRVSPGAVLH I EDGDLVQR GDNLVLLVFE RAKTGDIVQG LPRIEELLEA RKPKEACVLA RAPGVCQVEY LEDESVDIKV VEDDGTVSEY PL LPGQNAM VTDGQRIDVG HALTDGYNNP HEILDVFFSY YVDKDGCYQA ALRGLQAAQK FLVNEVQTVY QSQGVDISDK HIE VIVRQM TAKVRIDDGG DTTMLPGELV ELRQVEQVNE AMGITGSAPA RYTPVLLGIT KASLNTDSFI SAASFQETTR VLTE AAIEG KSDWLRGLKE NVIIGRLIPA GTGFSSHEEV LGLIETQDDI QGYMIEPIEL PTTKKKASAT KVKTKKVEAD DDLLD DTRA RAYAGTQLSQ DDEEFEETYD TDEDDFDMDD DDDFGDDED

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #7: Nontemplate strand DNA

MacromoleculeName: Nontemplate strand DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.81025 KDa
SequenceString: (DG)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DG) (DG)(DC)(DC)(DC)(DG)(DT)(DC)(DC)(DG)(DT) (DT)(DA)(DT)(DG)(DG)(DT)(DA)(DT)(DA) (DA)(DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT)(DG) (DT) (DC)(DA)(DC)(DG)(DG)(DA) ...String:
(DG)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DG) (DG)(DC)(DC)(DC)(DG)(DT)(DC)(DC)(DG)(DT) (DT)(DA)(DT)(DG)(DG)(DT)(DA)(DT)(DA) (DA)(DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT)(DG) (DT) (DC)(DA)(DC)(DG)(DG)(DA)(DT)(DG) (DC)(DA)(DG)(DG)(DT)(DG)(DG)(DC)(DT)(DG) (DG)(DT) (DT)(DC)(DT)(DC)(DG)(DC)(DG)

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Macromolecule #8: Template strand DNA

MacromoleculeName: Template strand DNA / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.673232 KDa
SequenceString: (DC)(DG)(DC)(DG)(DA)(DG)(DA)(DA)(DC)(DC) (DA)(DG)(DC)(DC)(DA)(DC)(DC)(DT)(DG)(DC) (DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA)(DG) (DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA)(DA) (DT) (DA)(DA)(DC)(DC)(DA)(DT) ...String:
(DC)(DG)(DC)(DG)(DA)(DG)(DA)(DA)(DC)(DC) (DA)(DG)(DC)(DC)(DA)(DC)(DC)(DT)(DG)(DC) (DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA)(DG) (DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA)(DA) (DT) (DA)(DA)(DC)(DC)(DA)(DT)(DA)(DA) (DC)(DG)(DG)(DA)(DC)(DG)(DG)(DG)(DC)(DC) (DT)(DT) (DG)(DT)(DC)(DA)(DA)(DG)(DC)

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Macromolecule #9: RNA (5'-R(*UP*CP*GP*A)-3')

MacromoleculeName: RNA (5'-R(*UP*CP*GP*A)-3') / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.240802 KDa
SequenceString:
UCGA

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 3432 / Average electron dose: 53.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 473353
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4yln

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 157889
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.08)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8gzg:
Cryo-EM structure of Synechocystis sp. PCC 6803 RPitc

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