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- EMDB-7320: Mtb RNAP Holo/RbpA/double fork DNA -closed clamp -

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Basic information

Entry
Database: EMDB / ID: EMD-7320
TitleMtb RNAP Holo/RbpA/double fork DNA -closed clamp
Map dataprimary map
Sample
  • Complex: Mtb RNAP Holo/RbpA/double fork DNA
    • 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
    • Protein or peptide: RNA polymerase-binding protein RbpA
    • DNA: DNA (31-MER)
    • DNA: DNA (26-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsinitiation / transcription bubble / closed clamp / TRANSCRIPTION / transcription-dna complex
Function / homology
Function and homology information


response to water / bacterial-type RNA polymerase holo enzyme binding / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding ...response to water / bacterial-type RNA polymerase holo enzyme binding / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / nucleic acid binding / protein dimerization activity / response to antibiotic / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / 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-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / 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 / 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 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
RNA polymerase sigma factor SigA / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / 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 ...RNA polymerase sigma factor SigA / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit omega / 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 / RNA polymerase-binding protein RbpA / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsDarst SA / Campbell EA
Citation
Journal: Elife / Year: 2018
Title: Fidaxomicin jams RNA polymerase motions needed for initiation via RbpA contacts.
Authors: Hande Boyaci / James Chen / Mirjana Lilic / Margaret Palka / Rachel Anne Mooney / Robert Landick / Seth A Darst / Elizabeth A Campbell /
Abstract: Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor ...Fidaxomicin (Fdx) is an antimicrobial RNA polymerase (RNAP) inhibitor highly effective against RNAP in vitro, but clinical use of Fdx is limited to treating intestinal infections due to poor absorption. To identify the structural determinants of Fdx binding to RNAP, we determined the 3.4 Å cryo-electron microscopy structure of a complete RNAP holoenzyme in complex with Fdx. We find that the actinobacteria general transcription factor RbpA contacts fidaxomycin, explaining its strong effect on . Additional structures define conformational states of RNAP between the free apo-holoenzyme and the promoter-engaged open complex ready for transcription. The results establish that Fdx acts like a doorstop to jam the enzyme in an open state, preventing the motions necessary to secure promoter DNA in the active site. Our results provide a structural platform to guide development of anti-tuberculosis antimicrobials based on the Fdx binding pocket.
#1: Journal: To Be Published
Title: Structure of Mycobacterium Tuberculosis RNAP Holo Enzyme/RbpA in closed clamp conformation
Authors: Darst SA / Campbell EA / Boyaci Selcuk H / Chen J / Lilic M
History
DepositionDec 27, 2017-
Header (metadata) releaseMar 14, 2018-
Map releaseMar 28, 2018-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c04
  • Surface level: 0.55
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7320.png

Downloads & links

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Map

FileDownload / File: emd_7320.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.372 / Movie #1: 0.55
Minimum - Maximum-1.6567825 - 3.5391886
Average (Standard dev.)0.010567383 (±0.12062059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z330.000330.000330.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.6573.5390.011

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Supplemental data

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Sample components

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Entire : Mtb RNAP Holo/RbpA/double fork DNA

EntireName: Mtb RNAP Holo/RbpA/double fork DNA
Components
  • Complex: Mtb RNAP Holo/RbpA/double fork DNA
    • 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
    • Protein or peptide: RNA polymerase-binding protein RbpA
    • DNA: DNA (31-MER)
    • DNA: DNA (26-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Mtb RNAP Holo/RbpA/double fork DNA

SupramoleculeName: Mtb RNAP Holo/RbpA/double fork DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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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 (bacteria)
Molecular weightTheoretical: 37.745328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY ...String:
MLISQRPTLS EDVLTDNRSQ FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTEIILNL KSLVVSSEE DEPVTMYLRK QGPGEVTAGD IVPPAGVTVH NPGMHIATLN DKGKLEVELV VERGRGYVPA VQNRASGAEI G RIPVDSIY SPVLKVTYKV DATRVEQRTD FDKLILDVET KNSISPRDAL ASAGKTLVEL FGLARELNVE AEGIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPPSFDP SEV AGYDVA TGTWSTEGAY DEQDYAETEQ L

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 (bacteria)
Molecular weightTheoretical: 130.070797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV ...String:
MADSRQSKTA ASPSPSRPQS SSNNSVPGAP NRVSFAKLRE PLEVPGLLDV QTDSFEWLIG SPRWRESAAE RGDVNPVGGL EEVLYELSP IEDFSGSMSL SFSDPRFDDV KAPVDECKDK DMTYAAPLFV TAEFINNNTG EIKSQTVFMG DFPMMTEKGT F IINGTERV VVSQLVRSPG VYFDETIDKS TDKTLHSVKV IPSRGAWLEF DVDKRDTVGV RIDRKRRQPV TVLLKALGWT SE QIVERFG FSEIMRSTLE KDNTVGTDEA LLDIYRKLRP GEPPTKESAQ TLLENLFFKE KRYDLARVGR YKVNKKLGLH VGE PITSST LTEEDVVATI EYLVRLHEGQ TTMTVPGGVE VPVETDDIDH FGNRRLRTVG ELIQNQIRVG MSRMERVVRE RMTT QDVEA ITPQTLINIR PVVAAIKEFF GTSQLSQFMD QNNPLSGLTH KRRLSALGPG GLSRERAGLE VRDVHPSHYG RMCPI ETPE GPNIGLIGSL SVYARVNPFG FIETPYRKVV DGVVSDEIVY LTADEEDRHV VAQANSPIDA DGRFVEPRVL VRRKAG EVE YVPSSEVDYM DVSPRQMVSV ATAMIPFLEH DDANRALMGA NMQRQAVPLV RSEAPLVGTG MELRAAIDAG DVVVAEE SG VIEEVSADYI TVMHDNGTRR TYRMRKFARS NHGTCANQCP IVDAGDRVEA GQVIADGPCT DDGEMALGKN LLVAIMPW E GHNYEDAIIL SNRLVEEDVL TSIHIEEHEI DARDTKLGAE EITRDIPNIS DEVLADLDER GIVRIGAEVR DGDILVGKV TPKGETELTP EERLLRAIFG EKAREVRDTS LKVPHGESGK VIGIRVFSRE DEDELPAGVN ELVRVYVAQK RKISDGDKLA GRHGNKGVI GKILPVEDMP FLADGTPVDI ILNTHGVPRR MNIGQILETH LGWCAHSGWK VDAAKGVPDW AARLPDELLE A QPNAIVST PVFDGAQEAE LQGLLSCTLP NRDGDVLVDA DGKAMLFDGR SGEPFPYPVT VGYMYIMKLH HLVDDKIHAR ST GPYSMIT QQPLGGKAQF GGQRFGEMEC WAMQAYGAAY TLQELLTIKS DDTVGRVKVY EAIVKGENIP EPGIPESFKV LLK ELQSLC LNVEVLSSDG AAIELREGED EDLERAAANL GINLSRNESA SVEDLALARH GGS

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 (bacteria)
Molecular weightTheoretical: 148.202219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMLDVNFFD ELRIGLATAE DIRQWSYGEV KKPETINYRT LKPEKDGLFC EKIFGPTRDW ECYCGKYKRV RFKGIICERC GVEVTRAKV RRERMGHIEL AAPVTHIWYF KGVPSRLGYL LDLAPKDLEK IIYFAAYVIT SVDEEMRHNE LSTLEAEMAV E RKAVEDQR ...String:
GAMLDVNFFD ELRIGLATAE DIRQWSYGEV KKPETINYRT LKPEKDGLFC EKIFGPTRDW ECYCGKYKRV RFKGIICERC GVEVTRAKV RRERMGHIEL AAPVTHIWYF KGVPSRLGYL LDLAPKDLEK IIYFAAYVIT SVDEEMRHNE LSTLEAEMAV E RKAVEDQR DGELEARAQK LEADLAELEA EGAKADARRK VRDGGEREMR QIRDRAQREL DRLEDIWSTF TKLAPKQLIV DE NLYRELV DRYGEYFTGA MGAESIQKLI ENFDIDAEAE SLRDVIRNGK GQKKLRALKR LKVVAAFQQS GNSPMGMVLD AVP VIPPEL RPMVQLDGGR FATSDLNDLY RRVINRNNRL KRLIDLGAPE IIVNNEKRML QESVDALFDN GRRGRPVTGP GNRP LKSLS DLLKGKQGRF RQNLLGKRVD YSGRSVIVVG PQLKLHQCGL PKLMALELFK PFVMKRLVDL NHAQNIKSAK RMVER QRPQ VWDVLEEVIA EHPVLLNRAP TLHRLGIQAF EPMLVEGKAI QLHPLVCEAF NADFDGDQMA VHLPLSAEAQ AEARIL MLS SNNILSPASG RPLAMPRLDM VTGLYYLTTE VPGDTGEYQP ASGDHPETGV YSSPAEAIMA ADRGVLSVRA KIKVRLT QL RPPVEIEAEL FGHSGWQPGD AWMAETTLGR VMFNELLPLG YPFVNKQMHK KVQAAIINDL AERYPMIVVA QTVDKLKD A GFYWATRSGV TVSMADVLVP PRKKEILDHY EERADKVEKQ FQRGALNHDE RNEALVEIWK EATDEVGQAL REHYPDDNP IITIVDSGAT GNFTQTRTLA GMKGLVTNPK GEFIPRPVKS SFREGLTVLE YFINTHGARK GLADTALRTA DSGYLTRRLV DVSQDVIVR EHDCQTERGI VVELAERAPD GTLIRDPYIE TSAYARTLGT DAVDEAGNVI VERGQDLGDP EIDALLAAGI T QVKVRSVL TCATSTGVCA TCYGRSMATG KLVDIGEAVG IVAAQSIGEP GTQLTMRTFH QGGVGEDITG GLPRVQELFE AR VPRGKAP IADVTGRVRL EDGERFYKIT IVPDDGGEEV VYDKISKRQR LRVFKHEDGS ERVLSDGDHV EVGQQLMEGS ADP HEVLRV QGPREVQIHL VREVQEVYRA QGVSIHDKHI EVIVRQMLRR VTIIDSGSTE FLPGSLIDRA EFEAENRRVV AEGG EPAAG RPVLMGITKA SLATDSWLSA ASFQETTRVL TDAAINCRSD KLNGLKENVI IGKLIPAGTG INRYRNIAVQ PTEEA RAAA YTIPSYEDQY YSPDFGAATG AAVPLDDYGY SDYRHHHHHH HH

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 (bacteria)
Molecular weightTheoretical: 11.776996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSISQSDASL 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 (bacteria)
Molecular weightTheoretical: 58.169477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPHMAATKAS TATDEPVKRT ATKSPAASAS GAKTGAKRTA AKSASGSPPA KRATKPAARS VKPASAPQDT TTSTIPKRKT RAAAKSAAA KAPSARGHAT KPRAPKDAQH EAATDPEDAL DSVEELDAEP DLDVEPGEDL DLDAADLNLD DLEDDVAPDA D DDLDSGDD ...String:
GPHMAATKAS TATDEPVKRT ATKSPAASAS GAKTGAKRTA AKSASGSPPA KRATKPAARS VKPASAPQDT TTSTIPKRKT RAAAKSAAA KAPSARGHAT KPRAPKDAQH EAATDPEDAL DSVEELDAEP DLDVEPGEDL DLDAADLNLD DLEDDVAPDA D DDLDSGDD EDHEDLEAEA AVAPGQTADD DEEIAEPTEK DKASGDFVWD EDESEALRQA RKDAELTASA DSVRAYLKQI GK VALLNAE EEVELAKRIE AGLYATQLMT ELSERGEKLP AAQRRDMMWI CRDGDRAKNH LLEANLRLVV SLAKRYTGRG MAF LDLIQE GNLGLIRAVE KFDYTKGYKF STYATWWIRQ AITRAMADQA RTIRIPVHMV EVINKLGRIQ RELLQDLGRE PTPE ELAKE MDITPEKVLE IQQYAREPIS LDQTIGDEGD SQLGDFIEDS EAVVAVDAVS FTLLQDQLQS VLDTLSEREA GVVRL RFGL TDGQPRTLDE IGQVYGVTRE RIRQIESKTM SKLRHPSRSQ VLRDYLD

UniProtKB: RNA polymerase sigma factor SigA

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Macromolecule #6: RNA polymerase-binding protein RbpA

MacromoleculeName: RNA polymerase-binding protein RbpA / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 12.993695 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADRVLRGSR LGAVSYETDR NHDLAPRQIA RYRTDNGEEF EVPFADDAEI PGTWLCRNGM EGTLIEGDLP EPKKVKPPRT HWDMLLERR SIEELEELLK ERLELIRSRR RG

UniProtKB: RNA polymerase-binding protein RbpA

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Macromolecule #7: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 7 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 9.565193 KDa
SequenceString:
(DG)(DC)(DT)(DT)(DG)(DA)(DC)(DA)(DA)(DA) (DA)(DG)(DT)(DG)(DT)(DT)(DA)(DA)(DA)(DT) (DT)(DG)(DT)(DG)(DC)(DT)(DA)(DT)(DA) (DC)(DT)

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Macromolecule #8: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 8 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 7.930155 KDa
SequenceString:
(DA)(DG)(DC)(DA)(DC)(DA)(DA)(DT)(DT)(DT) (DA)(DA)(DC)(DA)(DC)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DA)(DA)(DG)(DC)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 6.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171547
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING

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