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- EMDB-0340: EM structure of the DNA wrapping in bacterial open transcription ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0340
TitleEM structure of the DNA wrapping in bacterial open transcription initiation complex
Map dataEM map of DNA wrapping in bacterial transcription initiation complex
Sample
  • Complex: E. coli RNAP-DNA wrapped open complex
    • Protein or peptide: RNA polymerase sigma factor RpoD
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • DNA: DNA (94-MER)
    • DNA: DNA (94-MER)
Function / homology
Function and homology information


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / 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 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / 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 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 Rpb6 / 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 beta / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria) / Escherichia coli K-12 (bacteria) / Enterobacteria phage lambda (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsFlorez-Ariza A / Cassago A / de Oliveira PSL / Guerra DG / Portugal RV
CitationJournal: Biorxiv / Year: 2020
Title: Interactions of Upstream and Downstream Promoter Regions with RNA Polymerase are Energetically Coupled and a Target of Regulation in Transcription Initiation
Authors: Sosa R / Florez-Ariza A / Diaz-Celis C / Onoa B / Cassago A / de Oliveira PSL / Portugal RV / Guerra DG / Bustamante C
History
DepositionNov 19, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseMay 27, 2020-
UpdateMay 27, 2020-
Current statusMay 27, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n4c
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0340.png

Downloads & links

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Map

FileDownload / File: emd_0340.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of DNA wrapping in bacterial transcription initiation complex
Voxel sizeX=Y=Z: 3.56 Å
Density
Contour LevelBy AUTHOR: 0.42 / Movie #1: 0.42
Minimum - Maximum-6.3740783 - 14.199835
Average (Standard dev.)0.7593058400 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.563.563.56
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z320.400320.400320.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-6.37414.2000.000

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Supplemental data

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Sample components

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Entire : E. coli RNAP-DNA wrapped open complex

EntireName: E. coli RNAP-DNA wrapped open complex
Components
  • Complex: E. coli RNAP-DNA wrapped open complex
    • Protein or peptide: RNA polymerase sigma factor RpoD
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • DNA: DNA (94-MER)
    • DNA: DNA (94-MER)

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Supramolecule #1: E. coli RNAP-DNA wrapped open complex

SupramoleculeName: E. coli RNAP-DNA wrapped open complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Wrapped transcription initiation open complex assembled between E. coli RNAP-sigma 70 holoenzyme and lambda PR wild-type promoter (+18 to -76)
Source (natural)Organism: Escherichia coli BL21 (bacteria)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: RNA polymerase sigma factor RpoD

MacromoleculeName: RNA polymerase sigma factor RpoD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 64.322277 KDa
SequenceString: QLKLLVTRGK EQGYLTYAEV NDHLPEDIVD SDQIEDIIQM INDMGIQVME EAPDADDLML AENTADEDAA EAAAQVLSSV ESEIGRTTD PVRMYMREMG TVELLTREGE IDIAKRIEDG INQVQCSVAE YPEAITYLLE QYDRVEAEEA RLSDLITGFV D PNAENSID ...String:
QLKLLVTRGK EQGYLTYAEV NDHLPEDIVD SDQIEDIIQM INDMGIQVME EAPDADDLML AENTADEDAA EAAAQVLSSV ESEIGRTTD PVRMYMREMG TVELLTREGE IDIAKRIEDG INQVQCSVAE YPEAITYLLE QYDRVEAEEA RLSDLITGFV D PNAENSID PELAREKFAE LRAQYVVTRD TIKAKGRSHA TAQEEILKLS EVFKQFRLVP KQFDYLVNSM RVMMDRVRTQ ER LIMKLCV EQCKMPKKNF ITLFTGNETS DTWFNAAIAM NKPWSEKLHD VSEEVHRALQ KLQQIEEETG LTIEQVKDIN RRM SIGEAK ARRAKKEMVE ANLRLVISIA KKYTNRGLQF LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA TWWIRQAITR SIAD QARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP EELAERMLMP EDKIRKVLKI SMETPIGDDE DSHLGIDFIE DTTSA TTES LRAATHDVLA GLTAREAKVL RMRFGIDMNT DYTLEEVGKQ FDVTRERIRQ IEAKALRKLR HPSRSEVLRS FLDD

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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: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 150.689672 KDa
SequenceString: VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK ...String:
VYSYTEKKRI RKDFGKRPQV LDVPYLLSIQ LDSFQKFIEQ DPEGQYGLEA AFRSVFPIQS YSGNSELQYV SYRLGEPVFD VQECQIRGV TYSAPLRVKL RLVIYEREAP EGTVKDIKEQ EVYMGEIPLM TDNGTFVING TERVIVSQLH RSPGVFFDSD K GKTHSSGK VLYNARIIPY RGSWLDFEFD PKDNLFVRID RRRKLPATII LRALNYTTEQ ILDLFFEKVI FEIRDNKLQM EL VPERLRG ETASFDIEAN GKVYVEKGRR ITARHIRQLE KDDVKLIEVP VEYIAGKVVA KDYIDESTGE LICAANMELS LDL LAKLSQ SGHKRIETLF TNDLDHGPYI SETLRVDPTN DRLSALVEIY RMMRPGEPPT REAAESLFEN LFFSEDRYDL SAVG RMKFN RSLLREEIEG SGILSKDDII DVMKKLIDIR NGKGEVDDID HLGNRRIRSV GEMAENQFRV GLVRVERAVK ERLSL GDLD TLMPQDMINA KPISAAVKEF FGSSQLSQFM DQNNPLSEIT HKRRISALGP GGLTRERAGF EVRDVHPTHY GRVCPI ETP EGPNIGLINS LSVYAQTNEY GFLETPYRKV TDGVVTDEIH YLSAIEEGNY VIAQANSNLD EEGHFVEDLV TCRSKGE SS LFSRDQVDYM DVSTQQVVSV GASLIPFLEH DDANRALMGA NMQRQAVPTL RADKPLVGTG MERAVAVDSG VTAVAKRG G VVQYVDASRI VIKVNEDEMY PGEAGIDIYN LTKYTRSNQN TCINQMPCVS LGEPVERGDV LADGPSTDLG ELALGQNMR VAFMPWNGYN FEDSILVSER VVQEDRFTTI HIQELACVSR DTKLGPEEIT ADIPNVGEAA LSKLDESGIV YIGAEVTGGD ILVGKVTPK GETQLTPEEK LLRAIFGEKA SDVKDSSLRV PNGVSGTVID VQVFTRDGVE KDKRALEIEE MQLKQAKKDL S EELQILEA GLFSRIRAVL VAGGVEAEKL DKLPRDRWLE LGLTDEEKQN QLEQLAEQYD ELKHEFEKKL EAKRRKITQG DD LAPGVLK IVKVYLAVKR RIQPGDKMAG RHGNKGVISK INPIEDMPYD ENGTPVDIVL NPLGVPSRMN IGQILETHLG MAA KGIGDK INAMLKQQQE VAKLREFIQR AYDLGADVRQ KVDLSTFSDE EVMRLAENLR KGMPIATPVF DGAKEAEIKE LLKL GDLPT SGQIRLYDGR TGEQFERPVT VGYMYMLKLN HLVDDKMHAR STGSYSLVTQ QPLGGKAQFG GQRFGEMEVW ALEAY GAAY TLQEMLTVKS DDVNGRTKMY KNIVDGNHQM EPGMPESFNV LLKEIRSLGI NIELEDE

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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: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 150.320219 KDa
SequenceString: EEFDAIKIAL ASPDMIRSWS FGEVKKPETI NYRTFKPERD GLFCARIFGP VKDYECLCGK YKRLKHRGVI CEKCGVEVTQ TKVRRERMG HIELASPTAH IWFLKSLPSR IGLLLDMPLR DIERVLYFES YVVIEGGMTN LERQQILTEE QYLDALEEFG D EFDAKMGA ...String:
EEFDAIKIAL ASPDMIRSWS FGEVKKPETI NYRTFKPERD GLFCARIFGP VKDYECLCGK YKRLKHRGVI CEKCGVEVTQ TKVRRERMG HIELASPTAH IWFLKSLPSR IGLLLDMPLR DIERVLYFES YVVIEGGMTN LERQQILTEE QYLDALEEFG D EFDAKMGA EAIQALLKSM DLEQECEQLR EELNETNSET KRKKLTKRIK LLEAFVQSGN KPEWMILTVL PVLPPDLRPL VP LDGGRFA TSDLNDLYRR VINRNNRLKR LLDLAAPDII VRNEKRMLQE AVDALLDNGR RGRAITGSNK RPLKSLADMI KGK QGRFRQ NLLGKRVDYS GRSVITVGPY LRLHQCGLPK KMALELFKPF IYGKLELRGL ATTIKAAKKM VEREEAVVWD ILDE VIREH PVLLNRAPTL HRLGIQAFEP VLIEGKAIQL HPLVCAAYNA DFDGDQMAVH VPLTLEAQLE ARALMMSTNN ILSPA NGEP IIVPSQDVVL GLYYMTRDCV NAKGMVLTGP AERLYRSGLA SLHARVKVRI TEYEKDANGE LVAKTSLKDT TVGRAI LWM IVPKGLPYSI VNQALGKKAI SKMLNTCYRI LGLKPTVIFA DQIMYTGFAY AARSGASVGI DDMVIPEKKH EIISEAE AE VAEIQEQFQS GLVTAGERYN KVIDIWAAAN DRVSKAMMDN LQTETVINRD GQEEKQVSFN SIYMMADSGA RGSAAQIR Q LAGMRGLMAK PDGSIIETPI TANFREGLNV LQYFISTHGA RKGLADTALK TANSGYLTRR LVDVAQDLVV TEDDCGTHE GIMMTPVIEG GDVKEPLRDR VLGRVTAEDV LKPGTADILV PRNTLLHEQW CDLLEENSVD AVKVRSVVSC DTDFGVCAHC YGRDLARGH IINKGEAIGV IAAQSIGEPG TQLTMRTFHI GGAASRAAAE SSIQVKNKGS IKLSNVKSVV NSSGKLVITS R NTELKLID EFGRTKESYK VPYGAVLAKG DGEQVAGGET VANWDPHTMP VITEVSGFVR FTDMIDGQTI TRQTDELTGL SS LVVLDSA ERTAGGKDLR PALKIVDAQG NDVLIPGTDM PAQYFLPGKA IVQLEDGVQI SSGDTLARIP QESGGTKDIT GGL PRVADL FEARRPKEPA ILAEISGIVS FGKETKGKRR LVITPVDGSD PYEEMIPKWR QLNVFEGERV ERGDVISDGP EAPH DILRL RGVHAVTRYI VNEVQDVYRL QGVKINDKHI EVIVRQMLRK ATIVNAGSSD FLEGEQVEYS RVKIANRELE ANGKV GATY SRDLLGITKA SLATESFISA ASFQETTRVL TEAAVAGKRD ELRGLKENVI VGRLIPAGTG YAYHQDRMRR RAAG

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Macromolecule #4: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 35.275273 KDa
SequenceString: TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV ...String:
TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV DACYSPVERI AYNVEAARVE QRTDLDKLVI EMETNGTIDP EEAIRRAATI LAEQLEAFVD LRDVRQPEVK EE KPEFDPI LLRPVDDLEL TVRSANCLKA EAIHYIGDLV QRTEVELLKT PNLGKKSLTE IKDVLASRGL SLGMRLENW

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Macromolecule #5: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 34.400266 KDa
SequenceString: TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV ...String:
TEFLKPRLVD IEQVSSTHAK VTLEPLERGF GHTLGNALRR ILLSSMPGCA VTEVEIDGVL HEYSTKEGVQ EDILEILLNL KGLAVRVQG KDEVILTLNK SGIGPVTAAD ITHDGDVEIV KPQHVICHLT DENASISMRI KVQRGRGYVP ASTRIHSEED E RPIGRLLV DACYSPVERI AYNVEAARVE QRTDLDKLVI EMETNGTIDP EEAIRRAATI LAEQLEAFVD LRDVRQPEVK EE KPEFDPI LLLPVDDLEL TVRSANCLKA EAIHYIGDLV QRTEVELLKT PNLGKKSLTE IKDVLASRGL SLG

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Macromolecule #6: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 10.118352 KDa
SequenceString:
ARVTVQDAVE KIGNRFDLVL VAARRARQMQ VGGKDPLVPE ENDKTTVIAL REIEEGLINN QILDVRERQE QQEQEAAELQ AVTAIAEGR R

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Macromolecule #7: DNA (94-MER)

MacromoleculeName: DNA (94-MER) / type: dna / ID: 7 / Details: NT strand DNA (94-MER) / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Enterobacteria phage lambda (virus)
Molecular weightTheoretical: 29.094617 KDa
SequenceString: (DA)(DA)(DT)(DC)(DT)(DA)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DA)(DA)(DG)(DG)(DG)(DA)(DT) (DA)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DA) (DA)(DC)(DA)(DC)(DC)(DG)(DT)(DG)(DC)(DG) (DT) (DG)(DT)(DT)(DG)(DA)(DC) ...String:
(DA)(DA)(DT)(DC)(DT)(DA)(DT)(DC)(DA)(DC) (DC)(DG)(DC)(DA)(DA)(DG)(DG)(DG)(DA)(DT) (DA)(DA)(DA)(DT)(DA)(DT)(DC)(DT)(DA) (DA)(DC)(DA)(DC)(DC)(DG)(DT)(DG)(DC)(DG) (DT) (DG)(DT)(DT)(DG)(DA)(DC)(DT)(DA) (DT)(DT)(DT)(DT)(DA)(DC)(DC)(DT)(DC)(DT) (DG)(DG) (DC)(DG)(DG)(DT)(DG)(DA)(DT) (DA)(DA)(DT)(DG)(DG)(DT)(DT)(DG)(DC)(DA) (DT)(DG)(DT) (DA)(DC)(DT)(DA)(DA)(DG) (DG)(DA)(DG)(DG)(DT)(DT)(DG)(DT)

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Macromolecule #8: DNA (94-MER)

MacromoleculeName: DNA (94-MER) / type: dna / ID: 8 / Details: T strand DNA (94-MER) / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Enterobacteria phage lambda (virus)
Molecular weightTheoretical: 28.890529 KDa
SequenceString: (DA)(DC)(DA)(DA)(DC)(DC)(DT)(DC)(DC)(DT) (DT)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DT)(DA)(DT) (DC)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DA) (DG) (DG)(DT)(DA)(DA)(DA)(DA) ...String:
(DA)(DC)(DA)(DA)(DC)(DC)(DT)(DC)(DC)(DT) (DT)(DA)(DG)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DA)(DC)(DC)(DA)(DT)(DT)(DA)(DT) (DC)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DA) (DG) (DG)(DT)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DT)(DC)(DA)(DA)(DC)(DA)(DC)(DG)(DC) (DA)(DC) (DG)(DG)(DT)(DG)(DT)(DT)(DA) (DG)(DA)(DT)(DA)(DT)(DT)(DT)(DA)(DT)(DC) (DC)(DC)(DT) (DT)(DG)(DC)(DG)(DG)(DT) (DG)(DA)(DT)(DA)(DG)(DA)(DT)(DT)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: Negatively stained EM specimens were prepared using a 2% uranyl acetate solution.
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeJEOL 2100
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 20.0 e/Å2

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Image processing

Particle selectionNumber selected: 60393
CTF correctionSoftware - Name: IMAGIC
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: IMAGIC
Final 3D classificationSoftware - Name: IMAGIC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Software - Name: IMAGIC / Number images used: 16015
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4yln

DetailsInitial fiting was done using manual fitting in Chimera. Yasara software was used for energy minimizaton of the DNA and RNAP coordinates model.
RefinementProtocol: OTHER
Output model

PDB-6n4c:
EM structure of the DNA wrapping in bacterial open transcription initiation complex

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