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- EMDB-50589: DNA-directed RNA polymerase with transcriptional activator PafBC -

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Basic information

Entry
Database: EMDB / ID: EMD-50589
TitleDNA-directed RNA polymerase with transcriptional activator PafBC
Map dataSharpened map.
Sample
  • Complex: DNA-directed RNA polymerase with transcriptional activator PafBC
    • 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: PafB
    • Protein or peptide: PafC
    • DNA: recA-op non-template strand
    • DNA: recA-op template strand
KeywordsRNAP / PafBC / sigma adaptation / WYL domain / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / bacterial-type RNA polymerase core enzyme binding / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription ...sigma factor activity / bacterial-type RNA polymerase core enzyme binding / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / response to antibiotic / DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
PafC, HTH domain / PafC helix-turn-helix domain / Protein PafC / : / WYL domain profile. / WYL domain / WYL domain / RNA polymerase-binding protein RbpA / RbpA superfamily / RNA polymerase-binding protein ...PafC, HTH domain / PafC helix-turn-helix domain / Protein PafC / : / WYL domain profile. / WYL domain / WYL domain / 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, 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 beta' / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / RNA polymerase-binding protein RbpA / Protein pafC / Transcriptional regulator-like protein / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZdanowicz R / Schilling CM / Rabl J / Mueller AU / Boehringer D / Glockshuber R / Weber-Ban E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_215606 Switzerland
CitationJournal: Sci Adv / Year: 2025
Title: Single-stranded DNA binding to the transcription factor PafBC triggers the mycobacterial DNA damage response.
Authors: Charlotte M Schilling / Rafal Zdanowicz / Julius Rabl / Andreas U Müller / Daniel Boehringer / Rudi Glockshuber / Eilika Weber-Ban /
Abstract: The DNA damage response in mycobacteria is controlled by the heterodimeric transcription factor PafBC, a member of the WYL domain-containing protein family. It has been shown that PafBC induces ...The DNA damage response in mycobacteria is controlled by the heterodimeric transcription factor PafBC, a member of the WYL domain-containing protein family. It has been shown that PafBC induces transcription of its regulon by reprogramming the housekeeping RNA polymerase holoenzyme to recognize PafBC-dependent promoters through sigma adaptation. However, the mechanism by which DNA damage is sensed and translated into PafBC activation has remained unclear. Here, we demonstrate that the binding of single-stranded DNA (ssDNA) to the WYL domains of PafBC activates the transcription factor. Our cryo-electron microscopy structure of full-length PafBC in its active conformation, bound to the transcription initiation complex, reveals a previously unknown mode of interaction between the ssDNA and the WYL domains. Using biochemical experiments, we show that short ssDNA fragments bind to PafBC dynamically, resulting in deactivation as ssDNA levels decrease postrepair. Our findings shed light on the mechanism linking DNA damage to PafBC activation and expand our understanding of WYL domain-containing proteins.
History
DepositionJun 10, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50589.png

Downloads & links

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Map

FileDownload / File: emd_50589.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 360 pix.
= 403.2 Å		1.12 Å/pix.
x 360 pix.
= 403.2 Å		1.12 Å/pix.
x 360 pix.
= 403.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-2.6755798 - 3.0796258
Average (Standard dev.)-0.000600859 (±0.052193746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 403.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map.

Fileemd_50589_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A.

Fileemd_50589_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_50589_half_map_2.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : DNA-directed RNA polymerase with transcriptional activator PafBC

EntireName: DNA-directed RNA polymerase with transcriptional activator PafBC
Components
  • Complex: DNA-directed RNA polymerase with transcriptional activator PafBC
    • 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: PafB
    • Protein or peptide: PafC
    • DNA: recA-op non-template strand
    • DNA: recA-op template strand

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Supramolecule #1: DNA-directed RNA polymerase with transcriptional activator PafBC

SupramoleculeName: DNA-directed RNA polymerase with transcriptional activator PafBC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (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 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDDD EPVTMYLRKQ GPGVVTAGDI VPPAGVTVHN PDMHIATLND KGKLEVELVV ERGRGYVPAV QNKASGAEIG RIPVDSIYSP ...String:
MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDDD EPVTMYLRKQ GPGVVTAGDI VPPAGVTVHN PDMHIATLND KGKLEVELVV ERGRGYVPAV QNKASGAEIG RIPVDSIYSP VLKVTYKVEA TRVEQRTDFD KLIIDVETKN SISPRDALAS AGGTLVELFG LARELNADSE HIEIGPSPAE ADHIASFALP IDDLDLTVRS YNCLKREGVH TVGELVARTE SDLLDIRNFG QKSIDEVKIK LHQLGLSLKD SPATFDPSEV AGYDAATGTW TSDAGYDLDD NQDYAETEQL

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 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIEDF SGSMSLSFSD PRFDEVKASV DECKDKDMTY AAPLFVTAEF INNNTGEIKS QTVFMGDFPM MTEKGTFIIN GTERVVVSQL ...String:
MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIEDF SGSMSLSFSD PRFDEVKASV DECKDKDMTY AAPLFVTAEF INNNTGEIKS QTVFMGDFPM MTEKGTFIIN GTERVVVSQL VRSPGVYFDE TIDKSTEKTL HSVKVIPGRG AWLEFDVDKR DTVGVRIDRK RRQPVTVLLK ALGWTNEQIV ERFGFSEIMM GTLEKDTTSG TDEALLDIYR KLRPGEPPTK ESAQTLLENL FFKEKRYDLA RVGRYKVNKK LGLNAGKPIT SSTLTEEDVV ATIEYLVRLH EGQTSMTVPG GVEVPVEVDD IDHFGNRRLR TVGELIQNQI RVGLSRMERV VRERMTTQDV EAITPQTLIN IRPVVAAIKE FFGTSQLSQF MDQNNPLSGL THKRRLSALG PGGLSRERAG LEVRDVHPSH YGRMCPIETP EGPNIGLIGS LSVYARVNPF GFIETPYRKV ENGVVTDQID YLTADEEDRH VVAQANSPTD ENGRFTEDRV MVRKKGGEVE FVSADQVDYM DVSPRQMVSV ATAMIPFLEH DDANRALMGA NMQRQAVPLV RSEAPLVGTG MELRAAIDAG DVVVADKTGV IEEVSADYIT VMADDGTRQS YRLRKFARSN HGTCANQRPI VDAGQRVEAG QVIADGPCTQ NGEMALGKNL LVAIMPWEGH NYEDAIILSN RLVEEDVLTS IHIEEHEIDA RDTKLGAEEI TRDIPNVSDE VLADLDERGI VRIGAEVRDG DILVGKVTPK GETELTPEER LLRAIFGEKA REVRDTSLKV PHGESGKVIG IRVFSREDDD ELPAGVNELV RVYVAQKRKI SDGDKLAGRH GNKGVIGKIL PVEDMPFLPD GTPVDIILNT HGVPRRMNIG QILETHLGWV AKAGWNIDVA AGVPDWASKL PEELYSAPAD STVATPVFDG AQEGELAGLL GSTLPNRDGE VMVDADGKST LFDGRSGEPF PYPVTVGYMY ILKLHHLVDD KIHARSTGPY SMITQQPLGG KAQFGGQRFG EMECWAMQAY GAAYTLQELL TIKSDDTVGR VKVYEAIVKG ENIPEPGIPE SFKVLLKELQ SLCLNVEVLS SDGAAIEMRD GDDEDLERAA ANLGINLSRN ESASVEDLA

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 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKIIY FAAYVITSVD DEMRHNELST LEAEMAVEKK AVEDQRDADL ...String:
MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRRE RMGHIELAAP VTHIWYFKGV PSRLGYLLDL APKDLEKIIY FAAYVITSVD DEMRHNELST LEAEMAVEKK AVEDQRDADL EARAQKLEAD LAELEAEGAK SDVRRKVRDS GEREMRQLRD RAQRELDRLD EIWNTFTKLA PKQLIVDEVL YRELQDRYGE YFTGAMGAES IKKLIENFDI DAEAESLREV IRSGKGQKKL RALKRLKVVA AFQQSGNSPM GMVLDAVPVI PPELRPMVQL DGGRFATSDL NDLYRRVINR NNRLKRLIDL GAPEIIVNNE KRMLQESVDA LFDNGRRGRP VTGPGNRPLK SLSDLLKGKQ GRFRQNLLGK RVDYSGRSVI VVGPQLKLHQ CGLPKLMALE LFKPFVMKRL VDLNHAQNIK SAKRMVERQR PQVWDVLEEV IAEHPVLLNR APTLHRLGIQ AFEPQLVEGK AIQLHPLVCE AFNADFDGDQ MAVHLPLSAE AQAEARILML SSNNILSPAS GKPLAMPRLD MVTGLYYLTT LVEGATGEYQ AATKDAPEQG VYSSPAEAIM AMDRGALSVR AKIKVRLTEL RPPTDLEAQL FENGWKPGDA WTAETTLGRV MFNELLPKSY PFVNEQMHKK VQARIINDLA ERFPMIVVAQ TVDKLKDAGF YWATRSGVTV SMADVLVPPQ KQEILERHEA EADAIERKYQ RGALNHTERN ESLVKIWQDA TEEVGKALEE FYPADNPIIT IVKSGATGNL TQTRTLAGMK GLVTNPKGEF IPRPIKSSFR EGLTVLEYFI NTHGARKGLA DTALRTADSG YLTRRLVDVS QDVIVREHDC ETERGINVTL AERGPDGTLI RDAHVETSAF ARTLATDAVD ANGNVIIERG HDLGDPAIDA LLAAGITTVK VRSVLTCTSA TGVCAMCYGR SMATGKLVDI GEAVGIVAAQ SIGEPGTQLT MRTFHQGGVT GGADIVGGLP RVQELFEARV PRNKAPIADV AGRVRLEESD KFFKITIVPD DGGEEVVYDK LSKRQRLRVI THEDGTEGVL SDGDHVEVGD QLMEGAADPH EVLRVQGPRE VQIHLVKEVQ EVYRAQGVSI HDKHIEVIVR QMLRRVTIID SGSTEFLPGS LTERAEFEAE NRRVVAEGGE PAAGRPVLMG ITKASLATDS WLSAASFQET TRVLTDAAIN CRSDKLNGLK ENVIIGKLIP AGTGISRYRN IQVQPTEEAR AAAYTIPSYE DQYYSPDFGQ ATGAAVPLDD YGYSDYRWSH PQFEKGGGSG GGSGGSAWSH PQFEK

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 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MSTPHADAQL NAADDLGIDS SAASAYDTPL GITNPPIDEL LSRASSKYAL VIYAAKRARQ INDYYNQLGD GILEYVGPLV EPGLQEKPLS IALREIHGDL LEHTEGE

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 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTDL ELDDLDSDDD TAVEDEEEEA DAATPAVATA KAADDDIDEP SEKDKASGDF VWDEEESEAL RQARKDAELT ASADSVRAYL ...String:
MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTDL ELDDLDSDDD TAVEDEEEEA DAATPAVATA KAADDDIDEP SEKDKASGDF VWDEEESEAL RQARKDAELT ASADSVRAYL KQIGKVALLN AEEEVELAKR IEAGLYATQK LAELAEKGEK LPVQQRRDMQ WICRDGDRAK NHLLEANLRL VVSLAKRYTG RGMAFLDLIQ EGNLGLIRAV EKFDYTKGYK FSTYATWWIR QAITRAMADQ ARTIRIPVHM VEVINKLGRI QRELLQDLGR EPTPEELAKE MDITPEKVLE IQQYAREPIS LDQTIGDEGD SQLGDFIEDS EAVVAVDAVS FTLLQDQLQS VLETLSEREA 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 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MADRVLRGSR LGAVSYETDR NHDLAPRQVA RYRTDNGEEF DVPFADDAEI PGTWLCRNGL EGTLIEGDVP EPKKVKPPRT HWDMLLERRS VEELEELLKE RLDLIKAKRR GTGS

UniProtKB: RNA polymerase-binding protein RbpA

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Macromolecule #7: PafB

MacromoleculeName: PafB / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GLSAVSKVER LMNLVIALLS TRTYLPAEKI RTTVAGYADS PSDEAFSRMF ERDKNELRDL GIPLETGRVS KWDSTEGYRI NRDSYALPPI GLTADEAAAV AVATQLWQSP ELVTATQNAV LKLRAAGVDV DADGVGVAIA STATLPGVRG SEEVLQSLLS AIDEGRAVQF ...String:
GLSAVSKVER LMNLVIALLS TRTYLPAEKI RTTVAGYADS PSDEAFSRMF ERDKNELRDL GIPLETGRVS KWDSTEGYRI NRDSYALPPI GLTADEAAAV AVATQLWQSP ELVTATQNAV LKLRAAGVDV DADGVGVAIA STATLPGVRG SEEVLQSLLS AIDEGRAVQF EHRPSRSADY TTRTVEPWGV VTHRGRWYLV GHDRDREDTR TFRLSRISAA ARPIGPAGAV QKPQDVNLRD IVRRAVAEQP TGERARIWIA GGRATALRRQ AVTSTPRTIG GRAGEEITVD IGTWDRLARE IASYGSDAVA LEPSSLRDDV VERLRAHAAG GER

UniProtKB: Transcriptional regulator-like protein

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Macromolecule #8: PafC

MacromoleculeName: PafC / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSQVSTRLVR LLNMVPYFQA NPKVTRAEAA AALGVTGKQL DADLDQLWMC GLPGYSPGDL IDFDFVGDTI EVTFSAGVDH PLRLTSTEAT GILVALRALV DVPGMVDPEA ARSAIAKIES AVGSQRAVVE GITEDTSAEP GAAATVRTAV RENRALTLEY YSASRDSLAT ...String:
MSQVSTRLVR LLNMVPYFQA NPKVTRAEAA AALGVTGKQL DADLDQLWMC GLPGYSPGDL IDFDFVGDTI EVTFSAGVDH PLRLTSTEAT GILVALRALV DVPGMVDPEA ARSAIAKIES AVGSQRAVVE GITEDTSAEP GAAATVRTAV RENRALTLEY YSASRDSLAT RTVDPIRVVL VGDNSYLEAW CRSAEAVRLF RFDRIVDAQL LDDPAAPPPP AVAAGPDTSL FDADPSLPSA TLLIGAAAAW MFDYYPLRDI TERPDGSCEA TMTYASEDWM ARFILGFGAE VQVLAPESLA TRVRQAAEAA LQAYARCV

UniProtKB: Protein pafC

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Macromolecule #9: recA-op non-template strand

MacromoleculeName: recA-op non-template strand / type: dna / ID: 9 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
GTGGTGAAGA GTTCGACCGG ACTTGTCGGT GGTCTGCTCT AACGTCACGG CCAACCGATC GGAACACC

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Macromolecule #10: recA-op template strand

MacromoleculeName: recA-op template strand / type: dna / ID: 10 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
GGTGTTCCGA TCGGTaccgg acatgtaaAG AGCAGACCAC CGACAAGTCC GGTCGAACTC TTCACCAC

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 78.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC Ab-Initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 470245
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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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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