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- EMDB-63701: Cryo-EM structure of Streptomyces coelicolor sigma factor shbA tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-63701
TitleCryo-EM structure of Streptomyces coelicolor sigma factor shbA transcription initiation complex with shbA promoter
Map data
Sample
  • Complex: Streptomyces coelicolor transcription initial 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: ECF sigma factor
    • DNA: DNA (27-MER)
    • DNA: DNA (31-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsDNA binding protein / RNA polymerase holoenzyme / TRANSCRIPTION / TRANSFERASE-DNA-RNA complex
Function / homology
Function and homology information


nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : ...nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / protein dimerization activity / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
RNA polymerase sigma-70 like / 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, subunit beta-prime, bacterial type ...RNA polymerase sigma-70 like / 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, 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 Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 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
DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta' / ECF sigma factor / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsLiu G / Zheng J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770068,32070040 China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes.
Authors: Guiyang Liu / Xu Yang / Wenjin Yan / Yiqun Wang / Feng Yu / Jianting Zheng /
Abstract: In bacteria, principal σ factors (σ70 or σA) transcribe housekeeping genes required for cell viability. Although most principal σ genes are transcribed by the RNA polymerase (RNAP) holoenzyme ...In bacteria, principal σ factors (σ70 or σA) transcribe housekeeping genes required for cell viability. Although most principal σ genes are transcribed by the RNA polymerase (RNAP) holoenzyme containing the principal σ factor itself, an extracytoplasmic function (ECF) σ factor (σShbA) governs transcription of the principal σ factor gene (hrdB) in two model Streptomycetes. Here, we employed a combination of cryo-electron microscopy (cryo-EM) and bioinformatics to decipher how σShbA-RNAP holoenzymes govern the transcription of hrdB genes in Streptomyces. A cryo-EM structure of Streptomyces coelicolor σShbA-RNAP-promoter open (RPo) complex was solved at 2.97 Å resolution. In combination with in vitro transcription assays, we demonstrate the unique structural features used by the σShbA to recognize the hrdB promoter and form a transcription bubble. All Streptomyces genomes (603) tagged as 'reference' were retrieved from NCBI Datasets. The conserved protein sequences and genomic neighborhoods, as well as the promoter consensus sequences of σShbA and σHrdB homologs, support that the principal σHrdB being governed by the ECF σShbA is a common feature in Streptomyces. Overall, these results provide detailed molecular insights into the transcription of the principal σHrdB gene and pave the way for globally modulating Streptomyces cell viability.
History
DepositionMar 11, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63701.png

Downloads & links

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Map

FileDownload / File: emd_63701.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å		0.89 Å/pix.
x 360 pix.
= 320.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.43321872 - 0.6992628
Average (Standard dev.)0.0008587869 (±0.012630541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63701_msk_1.map
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Half map: #2

Fileemd_63701_half_map_1.map
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Half map: #1

Fileemd_63701_half_map_2.map
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Sample components

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Entire : Streptomyces coelicolor transcription initial complex

EntireName: Streptomyces coelicolor transcription initial complex
Components
  • Complex: Streptomyces coelicolor transcription initial 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: ECF sigma factor
    • DNA: DNA (27-MER)
    • DNA: DNA (31-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Streptomyces coelicolor transcription initial complex

SupramoleculeName: Streptomyces coelicolor transcription initial complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Streptomyces coelicolor A3(2) (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: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 36.734641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY ...String:
MLIAQRPSLT EEVVDEFRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDLILNI KQLVVSSEH DEPVVMYLRK QGPGLVTAAD IAPPAGVEVH NPDLVLATLN GKGKLEMELT VERGRGYVSA VQNKQVGQEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIVDVET KQAMRPRDAM ASAGKTLVEL FGLARELNID AEGIDMGPSP TD AALAADL ALPIEELELT VRSYNCLKRE GIHSVGELVA RSEADLLDIR NFGAKSIDEV KAKLAGMGLA LKDSPPGFDP TAA ADAFGA DDDADAGFVE TEQY

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: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 128.644945 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAASRNASTA NTNNAASTAP LRISFAKIKE PLEVPNLLAL QTESFDWLLG NDAWKARVES ALESGQDVPT KSGLEEIFEE ISPIEDFSG SMSLTFRDHR FEPPKNSIDE CKDRDFTYAA PLFVTAEFTN NETGEIKSQT VFMGDFPLMT NKGTFVINGT E RVVVSQLV ...String:
MAASRNASTA NTNNAASTAP LRISFAKIKE PLEVPNLLAL QTESFDWLLG NDAWKARVES ALESGQDVPT KSGLEEIFEE ISPIEDFSG SMSLTFRDHR FEPPKNSIDE CKDRDFTYAA PLFVTAEFTN NETGEIKSQT VFMGDFPLMT NKGTFVINGT E RVVVSQLV RSPGVYFDSS IDKTSDKDIF SAKIIPSRGA WLEMEIDKRD MVGVRIDRKR KQSVTVLLKA LGWTTEQILE EF GEYESMR ATLEKDHTQG QDDALLDIYR KLRPGEPPTR EAAQTLLENL YFNPKRYDLA KVGRYKVNKK LGADEPLDAG VLT TDDVIA TIKYLVKLHA GETETVGESG REIVVETDDI DHFGNRRIRN VGELIQNQVR TGLARMERVV RERMTTQDVE AITP QTLIN IRPVVASIKE FFGTSQLSQF MDQNNPLSGL THKRRLNALG PGGLSRERAG FEVRDVHPSH YGRMCPIETP EGPNI GLIG SLASYGRINP FGFIETPYRK VVEGQVTDDV DYLTADEEDR FVIAQANAAL GDDMRFAEAR VLVRRRGGEV DYVPGD DVD YMDVSPRQMV SVATAMIPFL EHDDANRALM GANMMRQAVP LIKSESPLVG TGMEYRSAAD AGDVVKAEKA GVVQEVS AD YITTTNDDGT YITYRLAKFS RSNQGTSVNQ KVIVAEGDRI IEGQVLADGP ATENGEMALG KNLLVAFMPW EGHNYEDA I ILSQRLVQDD VLSSIHIEEH EVDARDTKLG PEEITRDIPN VSEEVLADLD ERGIIRIGAE VVAGDILVGK VTPKGETEL TPEERLLRAI FGEKAREVRD TSLKVPHGEI GKVIGVRVFD REEGDELPPG VNQLVRVYVA QKRKITDGDK LAGRHGNKGV ISKINPIED MPFLEDGTPV DIILNPLAVP SRMNPGQVLE IHLGWLASRG WDVSGLAEEW AQRLQVIGAD KVEPGTNVAT P VFDGARED ELAGLLQHTI PNRDGERMVL PSGKARLFDG RSGEPFPEPI SVGYMYILKL HHLVDDKLHA RSTGPYSMIT QQ PLGGKAQ FGGQRFGEME VWALEAYGAA YALQELLTIK SDDVTGRVKV YEAIVKGENI PEPGIPESFK VLIKEMQSLC LNV EVLSSD GMSIEMRDTD EDVFRAAEEL GIDLSRREPS SVEEV

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: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 144.807078 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLDVNFFDEL RIGLATADDI RQWSHGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKVI YFAAYMITFV DEERRTRDLP SLEAHVSVER Q QIEQRRDS ...String:
MLDVNFFDEL RIGLATADDI RQWSHGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKVI YFAAYMITFV DEERRTRDLP SLEAHVSVER Q QIEQRRDS DLEARAKKLE TDLAELEAEG AKADVRRKVR EGAEREMKQL RDRAQREIDR LDEVWNRFKN LKVQDLEGDE LL YRELRDR FGTYFDGSMG AAALQKRLES FDLDEEAERL REIIRTGKGQ KKTRALKRLK VVSAFLQTSN SPKGMVLDCV PVI PPDLRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LLDLGAPEII VNNEKRMLQE AVDALFDNGR RGRPVTGPGN RPLK SLSDM LKGKQGRFRQ NLLGKRVDYS ARSVIVVGPQ LKLHQCGLPK AMALELFKPF VMKRLVDLNH AQNIKSAKRM VERGR TVVY DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP QLVEGKAIQI HPLVCTAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILKPADGRP VTMPTQDMVL GLFFLTTDSE GRSPKGEGRA FGSSAEAIMA FDAGDLTLQA KIDIRFPVGT IPPRGFE PP AREEGEPEWQ QGDTFTLKTT LGRALFNELL PEDYPFVDYE VGKKQLSEIV NDLAERYPKV IVAATLDNLK AAGFFWAT R SGVTVAISDI VVPDAKKEIV KGYEGQDEKV QKQYERGLIT KEERTQELIA IWTKATNEVA EAMNDNFPKT NPVSMMVNS GARGNMMQMR QIAGMRGLVS NAKNETIPRP IKASFREGLS VLEYFISTHG ARKGLADTAL RTADSGYLTR RLVDVSQDVI IREEDCGTE RGLKLPIATR DADGTLRKAE DVETSVYARM LAEDVVIDGK VIAPANVDLG DVLIDALVAH GVEEVKTRSI L TCESQVGT CAMCYGRSLA TGKLVDIGEA VGIIAAQSIG EPGTQLTMRT FHTGGVAGDD ITQGLPRVVE LFEARTPKGV AP ISEASGR VRIEETEKTK KIVVTPDDGS DETAFPISKR ARLLVGEGDH VEVGQKLTVG ATNPHDVLRI LGQRAVQVHL VGE VQKVYN SQGVSIHDKH IEIIIRQMLR RVTIIESGDA ELLPGELVER TKFETENRRV VQEGGHPASG RPQLMGITKA SLAT ESWLS AASFQETTRV LTDAAINAKS DSLIGLKENV IIGKLIPAGT GLSRYRNIRV EPTEEAKAAM YSAVGYDDID YSPFG TGSG QAVPLEDYDY GPYNQ

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: ECF sigma factor

MacromoleculeName: ECF sigma factor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 21.357314 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRDDDAPPDQ GTVGGLVHRA VDGDEQATHD LLAHVHPLAL RYCRTRLSRL PGDARHFVED LAQEVCVAVL LALPRYKDTG RPFEAFVFA IAAHKVADLQ RAAMRHPGST AVPSDEMPER PDDSLGPEER ALLNSDAAWA KKLLANLPEN QRELLLLRIA V GLTAEETG ...String:
MRDDDAPPDQ GTVGGLVHRA VDGDEQATHD LLAHVHPLAL RYCRTRLSRL PGDARHFVED LAQEVCVAVL LALPRYKDTG RPFEAFVFA IAAHKVADLQ RAAMRHPGST AVPSDEMPER PDDSLGPEER ALLNSDAAWA KKLLANLPEN QRELLLLRIA V GLTAEETG QMLGMSPGAV RVAQHRALSR LRALAEQ

UniProtKB: ECF sigma factor

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Macromolecule #5: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 9.602186 KDa
SequenceString:
(DC)(DG)(DA)(DG)(DG)(DA)(DA)(DC)(DT)(DC) (DC)(DA)(DC)(DT)(DG)(DG)(DA)(DG)(DT)(DA) (DG)(DG)(DA)(DT)(DG)(DC)(DG)(DT)(DC) (DA)(DT)

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Macromolecule #6: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 9.575145 KDa
SequenceString:
(DA)(DT)(DG)(DA)(DC)(DG)(DC)(DA)(DT)(DC) (DC)(DT)(DT)(DG)(DA)(DG)(DG)(DT)(DG)(DT) (DG)(DG)(DA)(DG)(DT)(DT)(DC)(DC)(DT) (DC)(DG)

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: 2.7 / Energy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: PDB ENTRY
PDB model - PDB ID:

7x74

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85184
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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