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- EMDB-27487: P. gingivalis RNA Polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-27487
TitleP. gingivalis RNA Polymerase
Map dataP. gingivalis RNA polymerase
Sample
  • Complex: Porphyromonas gingivalis RNA polymerase
    • 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: RNA polymerase Rpb6
KeywordsPorphyromonas gingivalis / RNA polymerase / transcription / CFB group bacteria
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
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 ...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 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / 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, 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 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLiu B / Bu F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Mol Biol / Year: 2024
Title: Cryo-EM Structure of Porphyromonas gingivalis RNA Polymerase.
Authors: Fan Bu / Xiaoxuan Wang / Mengke Li / Li Ma / Chuan Wang / Yangbo Hu / Zhengguo Cao / Bin Liu /
Abstract: Porphyromonas gingivalis, an anaerobic CFB (Cytophaga, Fusobacterium, and Bacteroides) group bacterium, is the keystone pathogen of periodontitis and has been implicated in various systemic diseases. ...Porphyromonas gingivalis, an anaerobic CFB (Cytophaga, Fusobacterium, and Bacteroides) group bacterium, is the keystone pathogen of periodontitis and has been implicated in various systemic diseases. Increased antibiotic resistance and lack of effective antibiotics necessitate a search for new intervention strategies. Here we report a 3.5 Å resolution cryo-EM structure of P. gingivalis RNA polymerase (RNAP). The structure displays new structural features in its ω subunit and multiple domains in β and β' subunits, which differ from their counterparts in other bacterial RNAPs. Superimpositions with E. coli RNAP holoenzyme and initiation complex further suggest that its ω subunit may contact the σ4 domain, thereby possibly contributing to the assembly and stabilization of initiation complexes. In addition to revealing the unique features of P. gingivalis RNAP, our work offers a framework for future studies of transcription regulation in this important pathogen, as well as for structure-based drug development.
History
DepositionJul 5, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27487.png

Downloads & links

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Map

FileDownload / File: emd_27487.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationP. gingivalis RNA polymerase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 324 pix.
= 288.36 Å		0.89 Å/pix.
x 324 pix.
= 288.36 Å		0.89 Å/pix.
x 324 pix.
= 288.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.109
Minimum - Maximum-0.5716927 - 1.0922515
Average (Standard dev.)-0.00004832966 (±0.035250664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 288.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: P. gingivalis RNA polymerase-sharpened map

Fileemd_27487_additional_1.map
AnnotationP. gingivalis RNA polymerase-sharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_27487_half_map_1.map
Annotationhalf map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_27487_half_map_2.map
Annotationhalf map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Porphyromonas gingivalis RNA polymerase

EntireName: Porphyromonas gingivalis RNA polymerase
Components
  • Complex: Porphyromonas gingivalis RNA polymerase
    • 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: RNA polymerase Rpb6

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Supramolecule #1: Porphyromonas gingivalis RNA polymerase

SupramoleculeName: Porphyromonas gingivalis RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 389 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: Porphyromonas gingivalis (bacteria) / Strain: ATCC BAA-308 / W83
Molecular weightTheoretical: 36.838078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAILAFQKPE NVLMMETSDS IAKFEFKPLE PGYGITIGNA LRRILLSSLE GFAITAIKIE GVEHEFATIP GVLEDVTNII LNLKQVRFK QIVPNADVEK ATIVISNSEV FRAGDLNAQL SNFEVLNSNL VICHLDKSAT LTMEFSINKG RGYVSAEENR A EHNELSTI ...String:
MAILAFQKPE NVLMMETSDS IAKFEFKPLE PGYGITIGNA LRRILLSSLE GFAITAIKIE GVEHEFATIP GVLEDVTNII LNLKQVRFK QIVPNADVEK ATIVISNSEV FRAGDLNAQL SNFEVLNSNL VICHLDKSAT LTMEFSINKG RGYVSAEENR A EHNELSTI AIDSIYTPIR NVKYAVENFR VEQKTDYEKL LMEVTTDGSI RPVDALREAA QILISHFSLF AENKIAIEYV DI VDTDEFD EDSLHMRQLL KSKLSGLDLS VRALNCLNAA GVDTLGDLVS LSRSDLMKIR NFGKKSLTEL DELLATLNLS FGM DISKYK LDKD

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: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 142.524562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTPTTNNKRI NFASIKNPLF YPDFLEVQLK SFHDFLQLDT PPERRKKEGL YKVFAENFPI TDTRNNFVLE FLDYYIDPPK YSIEECLSR GLTYSVPLKA KLKLYCTDPD HEDFATVIQD VFLGPIPYMT SSGTFVINGA ERVIVSQLHR SPGVFFGQSL H TNGTKLYS ...String:
MTPTTNNKRI NFASIKNPLF YPDFLEVQLK SFHDFLQLDT PPERRKKEGL YKVFAENFPI TDTRNNFVLE FLDYYIDPPK YSIEECLSR GLTYSVPLKA KLKLYCTDPD HEDFATVIQD VFLGPIPYMT SSGTFVINGA ERVIVSQLHR SPGVFFGQSL H TNGTKLYS ARIIPFKGSW IEFATDINNV MYAYIDRKKK LPVTTLLRAI GFEADKDILD IFNLADEVKV TKANLKKCIG RK LAARVIN TYIDDLSDED TGEVVSMERI TVVVDREVEL TEDNIEAILN SNAQTILLHR NDSNTSDYSI IFNTLQKDPC NSE KEALYY VYRQLRNAEP ADDASAREVI TNLFFSDKRY DLGDVGRYRI NKKLNLNIDP DIKVLTNEDI IEIIKYLIEL VNSK ASVDD IDHLSNRRVR TVGEQLYNQF GIGLARMART VRDRMNVRDN EVFTPIDLVN AKTISSVVNS FFGTNALSQF MDQTN PLAE ITHKRRLSAL GPGGLSRERA GFEVRDVHYT HYGRLCPIET PEGPNIGLIS SLCVYAKISD LGFITTPYRE VKNGKV DFS DNGLKYYTAE EEEEKTVAQG NAPLDENGRF VRERVKARYE SDFPLVTPDE VDLMDVSPTQ IASIAAALIP FLEHDDA NR ALMGSNMMRQ AVPLLRPESP IVGTGIEGKL VKDSRTQIVA ERGGEVVFVD ASCIKIRYDR TADEEFVSFD DAIVTYYL P KYRKTNQSTT IDLHPICSKG DRVEAGQILT EGYSTQGGEL ALGRNVQVAY MPWKGYNYED AIVLNERMVR EDFFTSVHV DEYILEVRET KRGLEELTSD IPNVSEDATR DLDENGIVRI GAHIEPGDIL IGKITPKGES DPTPEEKLLR AIFGDKAGDV KDASLKATP SLRGVVIDTK LFSKAAKKKS RTSTKEAVSK LDETYAKRQQ QLHERLIEKL TELTKGKTCC GVKDYLNVEL I KAGSKFTK KDLEALDFNV IQLSDWTNDA HTNELIKAVA VNYLKHSKEI EAELRRRKLD ETIGDELPAG IVQMAKVYIA KK RKIQVGD KMAGRHGNKG IVSKIVRQED MPFLADGTPV DICLNPLGVP SRMNLGQIFE AVLAWAGRKM NVKFATPIFD GAS LNDMNE WTDKAGLPRD GKTYLYDGGT GERFDQPATV GVTYFLKLGH MVDDKMHARS IGPYSLITQQ PLGGKAQFGG QRFG EMEVW ALEAFGASHI LQEILTVKSD DVVGRSKAYE AIVKGDPMPT PGIPESLNVL LHELKGLGLS FSLD

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: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 161.311781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAFRKENKIK NNFSKIRITL ASPEEILENS FGEVLKPETI NYRTYKPERD GLFCERIFGP VKDFECHCGK YKRIRYRGIV CDRCGVEVT EKKVRRERMG HIHLVVPVAH IWYFRSLPNK IGYLLGLPTK KLDAIIYYER YVVIQPGVAE GLSQLDLLSE E EYLDKLDE ...String:
MAFRKENKIK NNFSKIRITL ASPEEILENS FGEVLKPETI NYRTYKPERD GLFCERIFGP VKDFECHCGK YKRIRYRGIV CDRCGVEVT EKKVRRERMG HIHLVVPVAH IWYFRSLPNK IGYLLGLPTK KLDAIIYYER YVVIQPGVAE GLSQLDLLSE E EYLDKLDE IERTHKGNQN LEDTNPDKFI AKIGAEAIYD LLCRVDLDSI SYELRDRANT DGSQQRKTEA LKRLQVVESF RA SKGVNRP EWMVMKVIPV IPPDLRPLVP LDGGRFATSD LNDLYRRVII RNNRLKRLIE IKAPEVILRN EKRMLQEAVD SLF DNSRKS SAVKSDNNRP LKSLSDSLKG KQGRFRQNLL GKRVDYSARS VIVVGPELKM HECGLPKDMA AELYKPFIIR KLIE RGIVK TVKSAKKIVD RKEPVIWDIL EYVMKGHPVL LNRAPTLHRL GIQAFQPKLI EGKAIQLHPL SCTAFNADFD GDQMA VHLP LSNEAILEAQ LLMLASHNIL NPANGAPITV PSQDMVLGLY YITKLRPNTK GHGLIFYGPE EATIAYNEGK VDIHAP IKV YVEDYENGEL VRRMVETSVG RLMVNEYVPK KVGYVNEVLG KKALRDIIGS VIKICGVATT AKFLDDIKNL GYYMAFK GG LSFNLADVLI PDEKDQLIQE GYTAVEQIMQ DYSMGFITFN ERYNQIIDTW THINGRLSNV LIKQLSSDND GFNSVFMM M DSGARGSKEQ IRQLSGMRGL MAKPQKSGAE GGQIIENPIL SNFKEGLSVL EYFISTHGAR KGLADTALKT ADAGYLTRR LVDVSHDVII TEEDCGTLRG LLTTELKQNE DVVASLYERI LGRVSVHDII HPTTGDIIVR AGEEIREQAA QIIEDSPIEA VEIRSVLTC ESKKGVCAKC YGRNLATNRM VQRGEVVGVI AAQSIGEPGT QLTLRTFHVG GIASNVATEN SLLSKYDGIL E FEELRAVD ATDESHQVVV SRMTELRIAD PNTGIILANH NIPYGAKLFF RQGDAVKKGD KIIEWDPFNA VIVSEVAGTL SF EGVVENV TFKMESDETT GLKEKIIIES KDKTMAPYAR IIDENGEMLK NYSLPMGAHV VKDDGDTVKV GEILVKIPRS VGK AGDITG GLPRVTELFE ARNPSNPAIV SEIDGEIGFG KLKRGNREIT VTSKLGEEKK YLIPLSKQLL VQENDFVRAG TPLS DGAIT PADILAIKGP TAVQEYIVNE VQDVYRLQGV KINDKHFEVI VRQMMRKVEI VDPGDTLFLE QQVVDKFEVM EENDR IWGK KVVIDAGDSQ VLKAGQIVTA RKLRDENSML KRKDLKIVKV RDAKSATASQ ILQGITRAAL QTKSFMSAAS FQETTK VLN EAAICGKTDY LEGLKENVIC GHLIPAGTGL RDYEKLVVMH RDDYEKATAE RKSFLSEPTA EPAMEEAPSE HHHHHH

UniProtKB: DNA-directed RNA polymerase subunit beta'

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Macromolecule #4: RNA polymerase Rpb6

MacromoleculeName: RNA polymerase Rpb6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyromonas gingivalis (bacteria)
Molecular weightTheoretical: 12.932515 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MELKKMNVPM DTITRDMVRL SEDTENVYET VMIIAKRANQ IGQQMKQDLE KKLQDFSSSN DNLEEVFENR EQIEISRYYE HLPKPGLIA TAEYEQDKLY HRMPGATSTN D

UniProtKB: DNA-directed RNA polymerase subunit omega

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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

Concentration4 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5 mM DTT, 8mM CHAPSO
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: NITROGEN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 32.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 137270
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-8dkc:
P. gingivalis RNA Polymerase

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