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- EMDB-72645: Cryo-EM structure of Mycobacterium tuberculosis transcription ini... -

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Basic information

Entry
Database: EMDB / ID: EMD-72645
TitleCryo-EM structure of Mycobacterium tuberculosis transcription initiation complex containing 2nt RNA in complex with UMN141
Map data
Sample
  • Complex: Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with UMN141
    • Protein or peptide: x 5 types
    • DNA: x 2 types
    • RNA: x 1 types
  • Ligand: x 3 types
KeywordsTranscription initiation complex / Mycobacterium tuberculosis / UMN141 / Inhibitor / Antibacterial agent / TRANSCRIPTION / TRANSFERASE-DNA-RNA-INHIBITOR complex
Function / homology
Function and homology information


response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor antagonist complex / peptidoglycan-based cell wall / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / bacterial-type RNA polymerase core enzyme binding / DNA-templated transcription elongation / DNA-templated transcription initiation / ribonucleoside binding ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor antagonist complex / peptidoglycan-based cell wall / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / bacterial-type RNA polymerase core enzyme binding / DNA-templated transcription elongation / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, funnel domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / 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
RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsYou LL / Ebright RH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure-Driven Reengineering of Rifabutin Analogs Restores Activity Against Multidrug-Resistant Tuberculosis
Authors: You LL / Ebright RH
History
DepositionSep 9, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72645.png

Downloads & links

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Map

FileDownload / File: emd_72645.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 560 pix.
= 285.04 Å		0.51 Å/pix.
x 560 pix.
= 285.04 Å		0.51 Å/pix.
x 560 pix.
= 285.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.509 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.07976303 - 0.22280881
Average (Standard dev.)0.0012990256 (±0.008421914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 285.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72645_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72645_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_72645_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis transcription initiation complex conta...

EntireName: Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with UMN141
Components
  • Complex: Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with UMN141
    • 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 (53-MER)
    • DNA: DNA (53-MER)
    • RNA: RNA (5'-R(*GP*A)-3')
  • Ligand: (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadeca[1,11,13]trienoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl [(8R)-5,6-dimethylpyrazolo[1,5-a]pyrimidin-3-yl]carbamate
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mycobacterium tuberculosis transcription initiation complex conta...

SupramoleculeName: Mycobacterium tuberculosis transcription initiation complex containing 2ntRNA in complex with UMN141
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 400 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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 40.279039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMLISQRPTL SEDVLTDNRS QFVIEPLEPG FGYTLGNSLR RTLLSSIPGA AVTSIRIDGV LHEFTTVPG VKEDVTEIIL NLKSLVVSSE EDEPVTMYLR KQGPGEVTAG DIVPPAGVTV HNPGMHIATL NDKGKLEVEL V VERGRGYV ...String:
MGHHHHHHHH HHSSGHIEGR HMLISQRPTL SEDVLTDNRS QFVIEPLEPG FGYTLGNSLR RTLLSSIPGA AVTSIRIDGV LHEFTTVPG VKEDVTEIIL NLKSLVVSSE EDEPVTMYLR KQGPGEVTAG DIVPPAGVTV HNPGMHIATL NDKGKLEVEL V VERGRGYV PAVQNRASGA EIGRIPVDSI YSPVLKVTYK VDATRVEQRT DFDKLILDVE TKNSISPRDA LASAGKTLVE LF GLARELN VEAEGIEIGP SPAEADHIAS FALPIDDLDL TVRSYNCLKR EGVHTVGELV ARTESDLLDI RNFGQKSIDE VKI KLHQLG LSLKDSPPSF DPSEVAGYDV ATGTWSTEGA YDEQDYAETE QL

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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 129.632328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MILADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYEL SPIEDFSGSM SLSFSDPRFD DVKAPVDECK DKDMTYAAPL FVTAEFINNN TGEIKSQTVF MGDFPMMTEK G TFIINGTE ...String:
MILADSRQSK TAASPSPSRP QSSSNNSVPG APNRVSFAKL REPLEVPGLL DVQTDSFEWL IGSPRWRESA AERGDVNPVG GLEEVLYEL SPIEDFSGSM SLSFSDPRFD DVKAPVDECK DKDMTYAAPL FVTAEFINNN TGEIKSQTVF MGDFPMMTEK G TFIINGTE RVVVSQLVRS PGVYFDETID KSTDKTLHSV KVIPSRGAWL EFDVDKRDTV GVRIDRKRRQ PVTVLLKALG WT SEQIVER FGFSEIMRST LEKDNTVGTD EALLDIYRKL RPGEPPTKES AQTLLENLFF KEKRYDLARV GRYKVNKKLG LHV GEPITS STLTEEDVVA TIEYLVRLHE GQTTMTVPGG VEVPVETDDI DHFGNRRLRT VGELIQNQIR VGMSRMERVV RERM TTQDV EAITPQTLIN IRPVVAAIKE FFGTSQLSQF MDQNNPLSGL THKRRLSALG PGGLSRERAG LEVRDVHPSH YGRMC PIET PEGPNIGLIG SLSVYARVNP FGFIETPYRK VVDGVVSDEI VYLTADEEDR HVVAQANSPI DADGRFVEPR VLVRRK AGE VEYVPSSEVD YMDVSPRQMV SVATAMIPFL EHDDANRALM GANMQRQAVP LVRSEAPLVG TGMELRAAID AGDVVVA EE SGVIEEVSAD YITVMHDNGT RRTYRMRKFA RSNHGTCANQ CPIVDAGDRV EAGQVIADGP CTDDGEMALG KNLLVAIM P WEGHNYEDAI ILSNRLVEED VLTSIHIEEH EIDARDTKLG AEEITRDIPN ISDEVLADLD ERGIVRIGAE VRDGDILVG KVTPKGETEL TPEERLLRAI FGEKAREVRD TSLKVPHGES GKVIGIRVFS REDEDELPAG VNELVRVYVA QKRKISDGDK LAGRHGNKG VIGKILPVED MPFLADGTPV DIILNTHGVP RRMNIGQILE THLGWCAHSG WKVDAAKGVP DWAARLPDEL L EAQPNAIV STPVFDGAQE AELQGLLSCT LPNRDGDVLV DADGKAMLFD GRSGEPFPYP VTVGYMYIMK LHHLVDDKIH AR STGPYSM ITQQPLGGKA QFGGQRFGEM ECWAMQAYGA AYTLQELLTI KSDDTVGRVK VYEAIVKGEN IPEPGIPESF KVL LKELQS LCLNVEVLSS DGAAIEEREG EDEDLERAAA NLGINLSRNE SASVEDLA

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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 147.068094 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVLDVNFFDE LRIGLATAED IRQWSYGEVK KPETINYRTL KPEKDGLFCE KIFGPTRDWE CYCGKYKRVR FKGIICERCG VEVTRAKVR RERMGHIELA APVTHIWYFK GVPSRLGYLL DLAPKDLEKI IYFAAYVITS VDEEMRHNEL STLEAEMAVE R KAVEDQRD ...String:
MVLDVNFFDE LRIGLATAED IRQWSYGEVK KPETINYRTL KPEKDGLFCE KIFGPTRDWE CYCGKYKRVR FKGIICERCG VEVTRAKVR RERMGHIELA APVTHIWYFK GVPSRLGYLL DLAPKDLEKI IYFAAYVITS VDEEMRHNEL STLEAEMAVE R KAVEDQRD GELEARAQKL EADLAELEAE GAKADARRKV RDGGEREMRQ IRDRAQRELD RLEDIWSTFT KLAPKQLIVD EN LYRELVD RYGEYFTGAM GAESIQKLIE NFDIDAEAES LRDVIRNGKG QKKLRALKRL KVVAAFQQSG NSPMGMVLDA VPV IPPELR PMVQLDGGRF ATSDLNDLYR RVINRNNRLK RLIDLGAPEI IVNNEKRMLQ ESVDALFDNG RRGRPVTGPG NRPL KSLSD LLKGKQGRFR QNLLGKRVDY SGRSVIVVGP QLKLHQCGLP KLMALELFKP FVMKRLVDLN HAQNIKSAKR MVERQ RPQV WDVLEEVIAE HPVLLNRAPT LHRLGIQAFE PMLVEGKAIQ LHPLVCEAFN ADFDGDQMAV HLPLSAEAQA EARILM LSS NNILSPASGR PLAMPRLDMV TGLYYLTTEV PGDTGEYQPA SGDHPETGVY SSPAEAIMAA DRGVLSVRAK IKVRLTQ LR PPVEIEAELF GHSGWQPGDA WMAETTLGRV MFNELLPLGY PFVNKQMHKK VQAAIINDLA ERYPMIVVAQ TVDKLKDA G FYWATRSGVT VSMADVLVPP RKKEILDHYE ERADKVEKQF QRGALNHDER NEALVEIWKE ATDEVGQALR EHYPDDNPI ITIVDSGATG NFTQTRTLAG MKGLVTNPKG EFIPRPVKSS FREGLTVLEY FINTHGARKG LADTALRTAD SGYLTRRLVD VSQDVIVRE HDCQTERGIV VELAERAPDG TLIRDPYIET SAYARTLGTD AVDEAGNVIV ERGQDLGDPE IDALLAAGIT Q VKVRSVLT CATSTGVCAT CYGRSMATGK LVDIGEAVGI VAAQSIGEPG TQLTMRTFHQ GGVGEDITGG LPRVQELFEA RV PRGKAPI ADVTGRVRLE DGERFYKITI VPDDGGEEVV YDKISKRQRL RVFKHEDGSE RVLSDGDHVE VGQQLMEGSA DPH EVLRVQ GPREVQIHLV REVQEVYRAQ GVSIHDKHIE VIVRQMLRRV TIIDSGSTEF LPGSLIDRAE FEAENRRVVA EGGE PAAGR PVLMGITKAS LATDSWLSAA SFQETTRVLT DAAINCRSDK LNGLKENVII GKLIPAGTGI NRYRNIAVQP TEEAR AAAY TIPSYEDQYY SPDFGAATGA AVPLDDYGYS DYR

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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 11.85114 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSISQSDASL AAVPAVDQFD PSSGASGGYD TPLGITNPPI DELLDRVSSK YALVIYAAKR ARQINDYYNQ LGEGILEYVG PLVEPGLQE KPLSIALREI HADLLEHTEG E

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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 58.791281 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADLNWMISV AATKASTATD EPVKRTATKS PAASASGAKT GAKRTAAKSA SGSPPAKRAT KPAARSVKPA SAPQDTTTST IPKRKTRAA AKSAAAKAPS ARGHATKPRA PKDAQHEAAT DPEDALDSVE ELDAEPDLDV EPGEDLGLDA ADLNLDDLED D VAPDADDD ...String:
MADLNWMISV AATKASTATD EPVKRTATKS PAASASGAKT GAKRTAAKSA SGSPPAKRAT KPAARSVKPA SAPQDTTTST IPKRKTRAA AKSAAAKAPS ARGHATKPRA PKDAQHEAAT DPEDALDSVE ELDAEPDLDV EPGEDLGLDA ADLNLDDLED D VAPDADDD LDSGDDEDHE GLEAEAAVAP GQTADDDEEI AEPTEKDKAS GDFVWDEDES EALRQARKDA ELTASADSVR AY LKQIGKV ALLNAEEEVE LAKRIEAGLY ATQLMTELSE RGEKLPAAQR RDMMWICRDG DRAKNHLLEA NLRLVVSLAK RYT GRGMAF LDLIQEGNLG LIRAVEKFDY TKGYKFSTYA TWWIRQAITR AMADQARTIR IPVHMVEVIN KLGRIQRELL QDLG REPTP EELAKEMDIT PEKVLEIQQY AREPISLDQT IGDEGDSQLG DFIEDSEAVV AVDAVSFTLL QDQLQSVLDT LSERE AGVV RLRFGLTDGQ PRTLDEIGQV YGVTRERIRQ IESKTMSKLR HPSRSQVLRD YLD

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 19.274336 KDa
SequenceString: (DG)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DG) (DG)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DG) (DG)(DC)(DC)(DC)(DG)(DT)(DC)(DC)(DG) (DT)(DT)(DG)(DC)(DC)(DG)(DT)(DA)(DT)(DA) (DA) (DT)(DG)(DG)(DG)(DA)(DG) ...String:
(DG)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DG) (DG)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DG) (DG)(DC)(DC)(DC)(DG)(DT)(DC)(DC)(DG) (DT)(DT)(DG)(DC)(DC)(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)

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Macromolecule #7: DNA (53-MER)

MacromoleculeName: DNA (53-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 19.118203 KDa
SequenceString: (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)(DG) (DG)(DC)(DA)(DA)(DC)(DG)(DG)(DA)(DC)(DG) (DG) (DG)(DC)(DC)(DT)(DT)(DG) ...String:
(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)(DG) (DG)(DC)(DA)(DA)(DC)(DG)(DG)(DA)(DC)(DG) (DG) (DG)(DC)(DC)(DT)(DT)(DG)(DT)(DC) (DA)(DA)(DG)(DC)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DG) (DC)(DC)

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Macromolecule #8: RNA (5'-R(*GP*A)-3')

MacromoleculeName: RNA (5'-R(*GP*A)-3') / type: rna / ID: 8 / Number of copies: 1
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 629.454 Da
SequenceString:
GA

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Macromolecule #9: (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6,18,20-trihydro...

MacromoleculeName: (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4- ...Name: (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6,18,20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-(2-methylpropyl)-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadeca[1,11,13]trienoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl [(8R)-5,6-dimethylpyrazolo[1,5-a]pyrimidin-3-yl]carbamate
type: ligand / ID: 9 / Number of copies: 1 / Formula: A1CSZ
Molecular weightTheoretical: 993.154 Da

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / 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: 57.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 431805
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Number images used: 94463
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9y78:
Cryo-EM structure of Mycobacterium tuberculosis transcription initiation complex containing 2nt RNA in complex with UMN141

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  • 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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