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- EMDB-47709: De Novo Mycobacterium tuberculosis transcription initiation pre-R... -

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Basic information

Entry
Database: EMDB / ID: EMD-47709
TitleDe Novo Mycobacterium tuberculosis transcription initiation pre-RPO promoter complex with open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Map dataDe Novo Mycobacterium tuberculosis transcription initiation pre-RPO promoter complex with open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Sample
  • Complex: Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA)
    • Protein or peptide: x 7 types
    • DNA: x 2 types
  • Ligand: x 2 types
KeywordsPromoter escape / transcription / De novo / RNA polymerase / Transcription-DNA complex
Function / homology
Function and homology information


SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity ...SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / sigma factor activity / ubiquitin-like protein ligase binding / rRNA transcription / bacterial-type RNA polymerase core enzyme binding / protein sumoylation / DNA-directed RNA polymerase complex / condensed nuclear chromosome / DNA-templated transcription initiation / ribonucleoside binding / protein tag activity / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
CarD-like, C-terminal domain / : / : / CarD, C-terminal domain / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain ...CarD-like, C-terminal domain / : / : / CarD, C-terminal domain / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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, 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, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / 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 Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / 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 / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta' / RNA polymerase-binding protein RbpA / RNA polymerase-binding transcription factor CarD / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBrewer JJ / Campbell EA / Darst SA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural Insights into De Novo Promoter Escape by Mycobacterium tuberculosis RNA Polymerase.
Authors: Joshua Brewer / Madeleine Delbeau / Winston Bates Zoullas / Seth A Darst / Elizabeth A Campbell /
Abstract: Transcription in bacteria is a multi-step process. In the first step, contacts between RNA polymerase and the promoter DNA must be established for transcription initiation to begin, but then these ...Transcription in bacteria is a multi-step process. In the first step, contacts between RNA polymerase and the promoter DNA must be established for transcription initiation to begin, but then these contacts must be broken for the enzyme to transition into the elongation phase. Single-molecule and biochemical observations report that promoter escape is a highly regulated and sometimes rate-limiting step in the transcription cycle; however, the structural mechanisms of promoter escape remain obscure. Promoter escape also serves as the target for the clinically important antibiotic rifampicin, used to treat tuberculosis. Here, we present seven distinct intermediates showing the structural details of M. tuberculosis RNA polymerase initial transcribing complexes and promoter escape, using a de novo cryo-electron microscopy approach. We describe the structural rearrangements that RNA polymerase undergoes to clear the promoter, including those required to release the initiation factor, σ, providing a structural account for decades of biochemical observations. These structures and supporting biochemistry provide a model of promoter escape, a universal step in the transcription cycle, with conformations that may be used to develop Rifampicin alternatives.
History
DepositionNov 5, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47709.png

Downloads & links

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Map

FileDownload / File: emd_47709.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDe Novo Mycobacterium tuberculosis transcription initiation pre-RPO promoter complex with open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.456 Å		1.08 Å/pix.
x 256 pix.
= 275.456 Å		1.08 Å/pix.
x 256 pix.
= 275.456 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.8073626 - 2.6710663
Average (Standard dev.)0.00429753 (±0.06299481)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_47709_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

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Half map: Half Map B

Fileemd_47709_half_map_1.map
AnnotationHalf Map B
Projections & Slices
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Half map: Half Map A

Fileemd_47709_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : Off-pathway Mycobacterium tuberculosis transcription initiation p...

EntireName: Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA)
Components
  • Complex: Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA)
    • 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
    • Protein or peptide: Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD
    • DNA: DNA (62-MER)
    • DNA: DNA (54-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Off-pathway Mycobacterium tuberculosis transcription initiation p...

SupramoleculeName: Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
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: 129.905672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEGCILADSR QSKTAASPSP SRPQSSSNNS VPGAPNRVSF AKLREPLEVP GLLDVQTDSF EWLIGSPRWR ESAAERGDVN PVGGLEEVL YELSPIEDFS GSMSLSFSDP RFDDVKAPVD ECKDKDMTYA APLFVTAEFI NNNTGEIKSQ TVFMGDFPMM T EKGTFIIN ...String:
MEGCILADSR QSKTAASPSP SRPQSSSNNS VPGAPNRVSF AKLREPLEVP GLLDVQTDSF EWLIGSPRWR ESAAERGDVN PVGGLEEVL YELSPIEDFS GSMSLSFSDP RFDDVKAPVD ECKDKDMTYA APLFVTAEFI NNNTGEIKSQ TVFMGDFPMM T EKGTFIIN GTERVVVSQL VRSPGVYFDE TIDKSTDKTL HSVKVIPSRG AWLEFDVDKR DTVGVRIDRK RRQPVTVLLK AL GWTSEQI VERFGFSEIM RSTLEKDNTV GTDEALLDIY RKLRPGEPPT KESAQTLLEN LFFKEKRYDL ARVGRYKVNK KLG LHVGEP ITSSTLTEED VVATIEYLVR LHEGQTTMTV PGGVEVPVET DDIDHFGNRR LRTVGELIQN QIRVGMSRME RVVR ERMTT QDVEAITPQT LINIRPVVAA IKEFFGTSQL SQFMDQNNPL SGLTHKRRLS ALGPGGLSRE RAGLEVRDVH PSHYG RMCP IETPEGPNIG LIGSLSVYAR VNPFGFIETP YRKVVDGVVS DEIVYLTADE EDRHVVAQAN SPIDADGRFV EPRVLV RRK AGEVEYVPSS EVDYMDVSPR QMVSVATAMI PFLEHDDANR ALMGANMQRQ AVPLVRSEAP LVGTGMELRA AIDAGDV VV AEESGVIEEV SADYITVMHD NGTRRTYRMR KFARSNHGTC ANQCPIVDAG DRVEAGQVIA DGPCTDDGEM ALGKNLLV A IMPWEGHNYE DAIILSNRLV EEDVLTSIHI EEHEIDARDT KLGAEEITRD IPNISDEVLA DLDERGIVRI GAEVRDGDI LVGKVTPKGE TELTPEERLL RAIFGEKARE VRDTSLKVPH GESGKVIGIR VFSREDEDEL PAGVNELVRV YVAQKRKISD GDKLAGRHG NKGVIGKILP VEDMPFLADG TPVDIILNTH GVPRRMNIGQ ILETHLGWCA HSGWKVDAAK GVPDWAARLP D ELLEAQPN AIVSTPVFDG AQEAELQGLL SCTLPNRDGD VLVDADGKAM LFDGRSGEPF PYPVTVGYMY IMKLHHLVDD KI HARSTGP YSMITQQPLG GKAQFGGQRF GEMECWAMQA YGAAYTLQEL LTIKSDDTVG RVKVYEAIVK GENIPEPGIP ESF KVLLKE LQSLCLNVEV LSSDGAAIEL REGEDEDLER AAANLGINLS RNESASVEDL A

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: 148.882969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LARHGGSGAM LDVNFFDELR IGLATAEDIR QWSYGEVKKP ETINYRTLKP EKDGLFCEKI FGPTRDWECY CGKYKRVRFK GIICERCGV EVTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKIIY FAAYVITSVD EEMRHNELST L EAEMAVER ...String:
LARHGGSGAM LDVNFFDELR IGLATAEDIR QWSYGEVKKP ETINYRTLKP EKDGLFCEKI FGPTRDWECY CGKYKRVRFK GIICERCGV EVTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKIIY FAAYVITSVD EEMRHNELST L EAEMAVER KAVEDQRDGE LEARAQKLEA DLAELEAEGA KADARRKVRD GGEREMRQIR DRAQRELDRL EDIWSTFTKL AP KQLIVDE NLYRELVDRY GEYFTGAMGA ESIQKLIENF DIDAEAESLR DVIRNGKGQK KLRALKRLKV VAAFQQSGNS PMG MVLDAV PVIPPELRPM VQLDGGRFAT SDLNDLYRRV INRNNRLKRL IDLGAPEIIV NNEKRMLQES VDALFDNGRR GRPV TGPGN RPLKSLSDLL KGKQGRFRQN LLGKRVDYSG RSVIVVGPQL KLHQCGLPKL MALELFKPFV MKRLVDLNHA QNIKS AKRM VERQRPQVWD VLEEVIAEHP VLLNRAPTLH RLGIQAFEPM LVEGKAIQLH PLVCEAFNAD FDGDQMAVHL PLSAEA QAE ARILMLSSNN ILSPASGRPL AMPRLDMVTG LYYLTTEVPG DTGEYQPASG DHPETGVYSS PAEAIMAADR GVLSVRA KI KVRLTQLRPP VEIEAELFGH SGWQPGDAWM AETTLGRVMF NELLPLGYPF VNKQMHKKVQ AAIINDLAER YPMIVVAQ T VDKLKDAGFY WATRSGVTVS MADVLVPPRK KEILDHYEER ADKVEKQFQR GALNHDERNE ALVEIWKEAT DEVGQALRE HYPDDNPIIT IVDSGATGNF TQTRTLAGMK GLVTNPKGEF IPRPVKSSFR EGLTVLEYFI NTHGARKGLA DTALRTADSG YLTRRLVDV SQDVIVREHD CQTERGIVVE LAERAPDGTL IRDPYIETSA YARTLGTDAV DEAGNVIVER GQDLGDPEID A LLAAGITQ VKVRSVLTCA TSTGVCATCY GRSMATGKLV DIGEAVGIVA AQSIGEPGTQ LTMRTFHQGG VGEDITGGLP RV QELFEAR VPRGKAPIAD VTGRVRLEDG ERFYKITIVP DDGGEEVVYD KISKRQRLRV FKHEDGSERV LSDGDHVEVG QQL MEGSAD PHEVLRVQGP REVQIHLVRE VQEVYRAQGV SIHDKHIEVI VRQMLRRVTI IDSGSTEFLP GSLIDRAEFE AENR RVVAE GGEPAAGRPV LMGITKASLA TDSWLSAASF QETTRVLTDA AINCRSDKLN GLKENVIIGK LIPAGTGINR YRNIA VQPT EEARAAAYTI PSYEDQYYSP DFGAATGAAV PLDDYGYSDY RHHHHHHHH

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: 11.85114 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 (bacteria)
Molecular weightTheoretical: 60.512031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHHH SSGLEVLFQG PHMAATKAST ATDEPVKRTA TKSPAASASG AKTGAKRTAA KSASGSPPAK RATKPAARSV KPASAPQDT TTSTIPKRKT RAAAKSAAAK APSARGHATK PRAPKDAQHE AATDPEDALD SVEELDAEPD LDVEPGEDLD L DAADLNLD ...String:
HHHHHHHHHH SSGLEVLFQG PHMAATKAST ATDEPVKRTA TKSPAASASG AKTGAKRTAA KSASGSPPAK RATKPAARSV KPASAPQDT TTSTIPKRKT RAAAKSAAAK APSARGHATK PRAPKDAQHE AATDPEDALD SVEELDAEPD LDVEPGEDLD L DAADLNLD DLEDDVAPDA DDDLDSGDDE DHEDLEAEAA VAPGQTADDD EEIAEPTEKD KASGDFVWDE DESEALRQAR KD AELTASA DSVRAYLKQI GKVALLNAEE EVELAKRIEA GLYATQLMTE LSERGEKLPA AQRRDMMWIC RDGDRAKNHL LEA NLRLVV SLAKRYTGRG MAFLDLIQEG NLGLIRAVEK FDYTKGYKFS TYATWWIRQA ITRAMADQAR TIRIPVHMVE VINK LGRIQ RELLQDLGRE PTPEELAKEM DITPEKVLEI QQYAREPISL DQTIGDEGDS QLGDFIEDSE AVVAVDAVSF TLLQD QLQS VLDTLSEREA GVVRLRFGLT DGQPRTLDEI GQVYGVTRER IRQIESKTMS KLRHPSRSQV LRDYLD

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: Ubiquitin-like protein SMT3,RNA polymerase-binding transcription ...

MacromoleculeName: Ubiquitin-like protein SMT3,RNA polymerase-binding transcription factor CarD
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 32.104199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMASMSDSEV NQEAKPEVKP EVKPETHINL KVSDGSSEIF FKIKKTTPLR RLMEAFAKRQ GKEMDSLRF LYDGIRIQAD QTPEDLDMED NDIIEAHREQ IGGSMIFKVG DTVVYPHHGA ALVEAIETRT IKGEQKEYLV L KVAQGDLT ...String:
MGHHHHHHHH HHSSGHIEGR HMASMSDSEV NQEAKPEVKP EVKPETHINL KVSDGSSEIF FKIKKTTPLR RLMEAFAKRQ GKEMDSLRF LYDGIRIQAD QTPEDLDMED NDIIEAHREQ IGGSMIFKVG DTVVYPHHGA ALVEAIETRT IKGEQKEYLV L KVAQGDLT VRVPAENAEY VGVRDVVGQE GLDKVFQVLR APHTEEPTNW SRRYKANLEK LASGDVNKVA EVVRDLWRRD QE RGLSAGE KRMLAKARQI LVGELALAES TDDAKAETIL DEVLAAAS

UniProtKB: Ubiquitin-like protein SMT3, RNA polymerase-binding transcription factor CarD

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Macromolecule #8: DNA (62-MER)

MacromoleculeName: DNA (62-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.31825 KDa
SequenceString: (DC)(DT)(DT)(DA)(DA)(DA)(DA)(DG)(DA)(DT) (DT)(DA)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DA) (DT)(DT)(DT)(DA)(DT)(DC)(DA)(DA)(DA) (DA)(DA)(DG)(DA)(DG)(DT)(DA)(DT)(DT)(DG) (DA) (DC)(DT)(DT)(DA)(DA)(DA) ...String:
(DC)(DT)(DT)(DA)(DA)(DA)(DA)(DG)(DA)(DT) (DT)(DA)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DA) (DT)(DT)(DT)(DA)(DT)(DC)(DA)(DA)(DA) (DA)(DA)(DG)(DA)(DG)(DT)(DA)(DT)(DT)(DG) (DA) (DC)(DT)(DT)(DA)(DA)(DA)(DG)(DT) (DC)(DT)(DA)(DA)(DC)(DC)(DT)(DA)(DT)(DA) (DG)(DG) (DA)(DT)(DA)(DC)(DT)(DT)(DA) (DC)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DG)(DA) (DG)(DA)(DG) (DG)(DG)(DA)(DC)(DA)(DC) (DG)(DG)(DC)(DG)(DA)(DA)(DT)(DA)(DG)(DC) (DC)(DA)(DT)(DC) (DC)(DC)(DA)(DA)(DT) (DC)(DG)(DA)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DG)(DT)(DC)(DG)(DG) (DG)(DA)(DT)(DC) (DT)(DG)(DG)

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Macromolecule #9: DNA (54-MER)

MacromoleculeName: DNA (54-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 39.053938 KDa
SequenceString: (DC)(DC)(DA)(DG)(DA)(DT)(DC)(DC)(DC)(DG) (DA)(DC)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DT) (DC)(DG)(DA)(DT)(DT)(DG)(DG)(DG)(DA) (DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT)(DC)(DG) (DC) (DC)(DG)(DT)(DG)(DT)(DC) ...String:
(DC)(DC)(DA)(DG)(DA)(DT)(DC)(DC)(DC)(DG) (DA)(DC)(DC)(DC)(DC)(DG)(DG)(DT)(DG)(DT) (DC)(DG)(DA)(DT)(DT)(DG)(DG)(DG)(DA) (DT)(DG)(DG)(DC)(DT)(DA)(DT)(DT)(DC)(DG) (DC) (DC)(DG)(DT)(DG)(DT)(DC)(DC)(DC) (DT)(DC)(DT)(DC)(DG)(DC)(DT)(DG)(DG)(DC) (DT)(DG) (DT)(DA)(DA)(DG)(DT)(DA)(DT) (DC)(DC)(DT)(DA)(DT)(DA)(DG)(DG)(DT)(DT) (DA)(DG)(DA) (DC)(DT)(DT)(DT)(DA)(DA) (DG)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DT)(DC) (DT)(DT)(DT)(DT) (DT)(DG)(DA)(DT)(DA) (DA)(DA)(DT)(DT)(DT)(DT)(DA)(DA)(DA)(DT) (DT)(DA)(DA)(DT)(DC) (DT)(DT)(DT)(DT) (DA)(DA)(DG)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.83 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: 0.4 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102319
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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