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- EMDB-30390: The cryo-EM structure of B. subtilis BmrR transcription activatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-30390
TitleThe cryo-EM structure of B. subtilis BmrR transcription activation complex
Map data
Sample
  • Complex: Bacillus subtilis BmrR transcription activation complex
    • Protein or peptide: x 7 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsRNA polymerase / Transcription activation / TRANSCRIPTION
Function / homology
Function and homology information


nucleoid / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity ...nucleoid / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-binding transcription factor activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. ...RNA polymerase epsilon subunit / RNA polymerase epsilon subunit / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / MerR-type HTH domain signature. / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Putative DNA-binding domain superfamily / 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, subunit beta-prime, bacterial type / 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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / 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 Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / 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 epsilon / DNA-directed RNA polymerase subunit omega / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / Multidrug-efflux transporter 1 regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria) / Bacillus subtilis (strain 168) (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsFang CL / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31822001 China
CitationJournal: Nat Commun / Year: 2020
Title: The bacterial multidrug resistance regulator BmrR distorts promoter DNA to activate transcription.
Authors: Chengli Fang / Linyu Li / Yihan Zhao / Xiaoxian Wu / Steven J Philips / Linlin You / Mingkang Zhong / Xiaojin Shi / Thomas V O'Halloran / Qunyi Li / Yu Zhang /
Abstract: The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure ...The MerR-family proteins represent a unique family of bacteria transcription factors (TFs), which activate transcription in a manner distinct from canonical ones. Here, we report a cryo-EM structure of a B. subtilis transcription activation complex comprising B. subtilis six-subunit (2αββ'ωε) RNA Polymerase (RNAP) core enzyme, σ, a promoter DNA, and the ligand-bound B. subtilis BmrR, a prototype of MerR-family TFs. The structure reveals that RNAP and BmrR recognize the upstream promoter DNA from opposite faces and induce four significant kinks from the -35 element to the -10 element of the promoter DNA in a cooperative manner, which restores otherwise inactive promoter activity by shortening the length of promoter non-optimal -35/-10 spacer. Our structure supports a DNA-distortion and RNAP-non-contact paradigm of transcriptional activation by MerR TFs.
History
DepositionJul 18, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00942
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00942
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ckq
  • Surface level: 0.00942
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30390.png

Downloads & links

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Map

FileDownload / File: emd_30390.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00942 / Movie #1: 0.00942
Minimum - Maximum-0.022576876 - 0.04441184
Average (Standard dev.)0.0001805755 (±0.0016370304)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0230.0440.000

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Supplemental data

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Sample components

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Entire : Bacillus subtilis BmrR transcription activation complex

EntireName: Bacillus subtilis BmrR transcription activation complex
Components
  • Complex: Bacillus subtilis BmrR transcription activation complex
    • 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 omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • Protein or peptide: Multidrug-efflux transporter 1 regulator
    • Protein or peptide: UPF0356 protein YkzG
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: TETRAPHENYLPHOSPHONIUM

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Supramolecule #1: Bacillus subtilis BmrR transcription activation complex

SupramoleculeName: Bacillus subtilis BmrR transcription activation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 480 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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 34.842387 KDa
SequenceString: MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS ...String:
MIEIEKPKIE TVEISDDAKF GKFVVEPLER GYGTTLGNSL RRILLSSLPG AAVTSIQIDG VLHEFSTIEG VVEDVTTIIL HIKKLALKI YSDEEKTLEI DVQGEGTVTA ADITHDSDVE ILNPDLHIAT LGENASFRVR LTAQRGRGYT PADANKRDDQ P IGVIPIDS IYTPVSRVSY QVENTRVGQV ANYDKLTLDV WTDGSTGPKE AIALGSKILT EHLNIFVGLT DEAQHAEIMV EK EEDQKEK VLEMTIEELD LSVRSYNCLK RAGINTVQEL ANKTEEDMMK VRNLGRKSLE EVKAKLEELG LGLRKDD

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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 133.847938 KDa
SequenceString: MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA ...String:
MTGQLVQYGR HRQRRSYARI SEVLELPNLI EIQTSSYQWF LDEGLREMFQ DISPIEDFTG NLSLEFIDYS LGEPKYPVEE SKERDVTYS APLRVKVRLI NKETGEVKDQ DVFMGDFPIM TDTGTFIING AERVIVSQLV RSPSVYFSGK VDKNGKKGFT A TVIPNRGA WLEYETDAKD VVYVRIDRTR KLPVTVLLRA LGFGSDQEIL DLIGENEYLR NTLDKDNTEN SDKALLEIYE RL RPGEPPT VENAKSLLDS RFFDPKRYDL ANVGRYKINK KLHIKNRLFN QRLAETLVDP ETGEILAEKG QILDRRTLDK VLP YLENGI GFRKLYPNGG VVEDEVTLQS IKIFAPTDQE GEQVINVIGN AYIEEEIKNI TPADIISSIS YFFNLLHGVG DTDD IDHLG NRRLRSVGEL LQNQFRIGLS RMERVVRERM SIQDTNTITP QQLINIRPVI ASIKEFFGSS QLSQFMDQTN PLAEL THKR RLSALGPGGL TRERAGMEVR DVHYSHYGRM CPIETPEGPN IGLINSLSSY AKVNRFGFIE TPYRRVDPET GKVTGR IDY LTADEEDNYV VAQANARLDD EGAFIDDSIV ARFRGENTVV SRNRVDYMDV SPKQVVSAAT ACIPFLENDD SNRALMG AN MQRQAVPLMQ PEAPFVGTGM EYVSGKDSGA AVICKHPGIV ERVEAKNVWV RRYEEVDGQK VKGNLDKYSL LKFVRSNQ G TCYNQRPIVS VGDEVVKGEI LADGPSMELG ELALGRNVMV GFMTWDGYNY EDAIIMSERL VKDDVYTSIH IEEYESEAR DTKLGPEEIT RDIPNVGEDA LRNLDDRGII RIGAEVKDGD LLVGKVTPKG VTELTAEERL LHAIFGEKAR EVRDTSLRVP HGGGGIIHD VKVFNREDGD ELPPGVNQLV RVYIVQKRKI SEGDKMAGRH GNKGVISKIL PEEDMPYLPD GTPIDIMLNP L GVPSRMNI GQVLELHMGM AARYLGIHIA SPVFDGAREE DVWETLEEAG MSRDAKTVLY DGRTGEPFDN RVSVGIMYMI KL AHMVDDK LHARSTGPYS LVTQQPLGGK AQFGGQRFGE MEVWALEAYG AAYTLQEILT VKSDDVVGRV KTYEAIVKGD NVP EPGVPE SFKVLIKELQ SLGMDVKILS GDEEEIEMRD LEDEEDAKQA DGLALSGDEE PEETASADVE RDVVTKE

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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 134.444953 KDa
SequenceString: MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA ...String:
MLDVNNFEYM NIGLASPDKI RSWSFGEVKK PETINYRTLK PEKDGLFCER IFGPTKDWEC HCGKYKRVRY KGVVCDRCGV EVTRAKVRR ERMGHIELAA PVSHIWYFKG IPSRMGLVLD MSPRALEEVI YFASYVVTDP ANTPLEKKQL LSEKEYRAYL D KYGNKFQA SMGAEAIHKL LQDIDLVKEV DMLKEELKTS QGQRRTRAIK RLEVLEAFRN SGNKPSWMIL DVLPVIPPEL RP MVQLDGG RFATSDLNDL YRRVINRNNR LKRLLDLGAP SIIVQNEKRM LQEAVDALID NGRRGRPVTG PGNRPLKSLS HML KGKQGR FRQNLLGKRV DYSGRSVIVV GPHLKMYQCG LPKEMALELF KPFVMKELVE KGLAHNIKSA KRKIERVQPE VWDV LESVI KEHPVLLNRA PTLHRLGIQA FEPTLVEGRA IRLHPLVCTA YNADFDGDQM AVHVPLSAEA QAEARILMLA AQNIL NPKD GKPVVTPSQD MVLGNYYLTL ERAGAVGEGM VFKNTDEALL AYQNGYVHLH TRVAVAANSL KNVTFTEEQR SKLLIT TVG KLVFNEILPE SFPYMNEPTK SNIEEKTPDR FFLEKGADVK AVIAQQPINA PFKKGILGKI IAEIFKRFHI TETSKML DR MKNLGFKYST KAGITVGVSD IVVLDDKQEI LEEAQSKVDN VMKQFRRGLI TEEERYERVI SIWSAAKDVI QGKLMKSL D ELNPIYMMSD SGARGNASNF TQLAGMRGLM ANPAGRIIEL PIKSSFREGL TVLEYFISTH GARKGLADTA LKTADSGYL TRRLVDVAQD VIIRETDCGT DRGILAKPLK EGTETIERLE ERLIGRFARK QVKHPETGEV LVNENELIDE DKALEIVEAG IEEVWIRSA FTCNTPHGVC KRCYGRNLAT GSDVEVGEAV GIIAAQSIGE PGTQLTMRTF HTGGVAGDDI TQGLPRIQEL F EARNPKGQ ATITEIDGTV VEINEVRDKQ QEIVVQGAVE TRSYTAPYNS RLKVAEGDKI TRGQVLTEGS IDPKELLKVT DL TTVQEYL LHEVQKVYRM QGVEIGDKHV EVMVRQMLRK VRVIDAGDTD VLPGTLLDIH QFTEANKKVL LEGNRPATGR PVL LGITKA SLETDSFLSA ASFQETTRVL TDAAIKGKRD ELLGLKENVI IGKLVPAGTG MMKYRKVKPV SNVQPTDDMV PVE

UniProtKB: DNA-directed RNA polymerase subunit beta'

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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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 7.766921 KDa
SequenceString:
MLDPSIDSLM NKLDSKYTLV TVSARRAREM QIKKDQMIEH TISHKYVGKA LEEIDAGLLS FEKEDRE

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: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 43.007406 KDa
SequenceString: MADKQTHETE LTFDQVKEQL TESGKKRGVL TYEEIAERMS SFEIESDQMD EYYEFLGEQG VELISENEET EDPNIQQLAK AEEEFDLND LSVPPGVKIN DPVRMYLKEI GRVNLLSAKE EIAYAQKIEE GDEESKRRLA EANLRLVVSI AKRYVGRGML F LDLIQEGN ...String:
MADKQTHETE LTFDQVKEQL TESGKKRGVL TYEEIAERMS SFEIESDQMD EYYEFLGEQG VELISENEET EDPNIQQLAK AEEEFDLND LSVPPGVKIN DPVRMYLKEI GRVNLLSAKE EIAYAQKIEE GDEESKRRLA EANLRLVVSI AKRYVGRGML F LDLIQEGN MGLMKAVEKF DYRKGYKFST YATWWIRQAI TRAIADQART IRIPVHMVET INKLIRVQRQ LLQDLGREPT PE EIAEDMD LTPEKVREIL KIAQEPVSLE TPIGEEDDSH LGDFIEDQEA TSPSDHAAYE LLKEQLEDVL DTLTDREENV LRL RFGLDD GRTRTLEEVG KVFGVTRERI RQIEAKALRK LRHPSRSKRL KDFLE

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #8: Multidrug-efflux transporter 1 regulator

MacromoleculeName: Multidrug-efflux transporter 1 regulator / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 32.951688 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GAMAMKESYY SIGEVSKLAN VSIKALRYYD KIDLFKPAYV DPDTSYRYYT DSQLIHLDLI KSLKYIGTPL EEMKKAQDLE MEELFAFYT EQERQIREKL DFLSALEQTI SLVKKRMKRQ MEYPALGEVF VLDEEEIRII QTEAEGIGPE NVLNASYSKL K KFIESADG ...String:
GAMAMKESYY SIGEVSKLAN VSIKALRYYD KIDLFKPAYV DPDTSYRYYT DSQLIHLDLI KSLKYIGTPL EEMKKAQDLE MEELFAFYT EQERQIREKL DFLSALEQTI SLVKKRMKRQ MEYPALGEVF VLDEEEIRII QTEAEGIGPE NVLNASYSKL K KFIESADG FTNNSYGATF SFQPYTSIDE MTYRHIFTPV LTNKQISSIT PDMEITTIPK GRYACIAYNF SPEHYFLNLQ KL IKYIADR QLTVVSDVYE LIIPIHYSPK KQEEYRVEMK IRIAE

UniProtKB: Multidrug-efflux transporter 1 regulator

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Macromolecule #9: UPF0356 protein YkzG

MacromoleculeName: UPF0356 protein YkzG / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria) / Strain: 168
Molecular weightTheoretical: 8.263358 KDa
SequenceString:
MIYKVFYQEK ADEVPVREKT DSLYIEGVSE RDVRTKLKEK KFNIEFITPV DGAFLEYEQQ SENFKVLEL

UniProtKB: DNA-directed RNA polymerase subunit epsilon

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Macromolecule #6: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.489907 KDa
SequenceString:
(DG)(DT)(DT)(DG)(DA)(DC)(DT)(DC)(DT)(DC) (DC)(DC)(DC)(DT)(DA)(DG)(DG)(DA)(DG)(DG) (DA)(DG)(DG)(DT)(DC)(DT)(DT)(DA)(DT) (DA)(DA)(DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT) (DG) (DT)(DC)(DA)(DC)(DG)(DG)(DA)(DT) (DG)(DC)

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Macromolecule #7: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.48594 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DC)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DC)(DG)(DA)(DG)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DA)(DA)(DG)(DA)(DC)(DC) (DT)(DC)(DC)(DT)(DC)(DC)(DT)(DA)(DG)(DG) (DG) (DG)(DA)(DG)(DA)(DG)(DT)(DC)(DA) (DA)(DC)

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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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Macromolecule #12: TETRAPHENYLPHOSPHONIUM

MacromoleculeName: TETRAPHENYLPHOSPHONIUM / type: ligand / ID: 12 / Number of copies: 2 / Formula: P4P
Molecular weightTheoretical: 339.389 Da
Chemical component information

ChemComp-P4P:
TETRAPHENYLPHOSPHONIUM

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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

Concentration19 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
50.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
3.0 mMC4H10O2S2DL-Dithiothreitol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 282.65 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) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2226 / Average exposure time: 7.6 sec. / Average electron dose: 60.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 494295
Startup modelType of model: EMDB MAP
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 103226
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6ldi

source_name: PDB, initial_model_type: experimental model

1exi

source_name: PDB, initial_model_type: experimental model

4njc

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7ckq:
The cryo-EM structure of B. subtilis BmrR transcription activation complex

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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