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- EMDB-34398: Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc -

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Basic information

Entry
Database: EMDB / ID: EMD-34398
TitleCryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc
Map data
Sample
  • Complex: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
    • Protein or peptide: x 6 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 3 types
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / 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-70 region 3 ...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 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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: 2.96 Å
AuthorsYou LL / Shen LQ / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc
Authors: You LL / Shen LQ / Zhang Y
History
DepositionSep 27, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34398.png

Downloads & links

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Map

FileDownload / File: emd_34398.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.0112
Minimum - Maximum-0.11300528 - 0.24922617
Average (Standard dev.)0.00032941645 (±0.0053237495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34398_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_34398_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34398_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34398_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc

EntireName: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
Components
  • Complex: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit gammaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • DNA: Nontemplate strand DNA
    • DNA: Template strand DNA
    • RNA: RNA (5'-R(*CP*CP*GP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE

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

SupramoleculeName: The complex of Synechocystis sp. PCC 6803 CTP-bound RPitc
type: complex / ID: 1 / Chimera: Yes / 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

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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

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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

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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

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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

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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

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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)(DA)(DG)(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)(DA)(DG)(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)(DG)(DA)(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)(DG)(DA)(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(*CP*CP*GP*A)-3')

MacromoleculeName: RNA (5'-R(*CP*CP*GP*A)-3') / type: rna / ID: 9 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.239818 KDa
SequenceString:
CCGA

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 2 / 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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Macromolecule #12: CYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: CTP
Molecular weightTheoretical: 483.156 Da
Chemical component information

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 135 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2297 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 681334
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.08)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 145731
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8gzh:
Cryo-EM structure of Synechocystis sp. PCC 6803 CTP-bound RPitc

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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