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- EMDB-13205: Mycobacterial RNAP with transcriptional activator PafBC -

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Basic information

Entry
Database: EMDB / ID: EMD-13205
TitleMycobacterial RNAP with transcriptional activator PafBC
Map datafull map, sharpened
Sample
  • Complex: DNA-directed RNA polymerase with transcriptional activator PafBC
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Ligand: x 1 types
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription ...bacterial-type RNA polymerase core enzyme binding / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 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 / 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 ...PafC, HTH domain / PafC helix-turn-helix domain / Protein PafC / 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 / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / 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 / 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: 3.2 Å
AuthorsMueller AU / Kummer E / Schilling CM / Ban N / Weber-Ban E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185250 Switzerland
CitationJournal: Sci Adv / Year: 2021
Title: Transcriptional control of mycobacterial DNA damage response by sigma adaptation.
Authors: Andreas U Müller / Eva Kummer / Charlotte M Schilling / Nenad Ban / Eilika Weber-Ban /
Abstract: Transcriptional activator PafBC is the key regulator of the mycobacterial DNA damage response and controls around 150 genes, including genes involved in the canonical SOS response, through an unknown ...Transcriptional activator PafBC is the key regulator of the mycobacterial DNA damage response and controls around 150 genes, including genes involved in the canonical SOS response, through an unknown molecular mechanism. Using a combination of biochemistry and cryo–electron microscopy, we demonstrate that PafBC in the presence of single-stranded DNA activates transcription by reprogramming the canonical −10 and −35 promoter specificity of RNA polymerase associated with the housekeeping sigma subunit. We determine the structure of this transcription initiation complex, revealing a unique mode of promoter recognition, which we term “sigma adaptation.” PafBC inserts between DNA and sigma factor to mediate recognition of hybrid promoters lacking the −35 but featuring the canonical −10 and a PafBC-specific −26 element. Sigma adaptation may constitute a more general mechanism of transcriptional control in mycobacteria.
History
DepositionJul 15, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 22, 2021-
Current statusDec 22, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p5x
  • Surface level: 0.35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13205.png

Downloads & links

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Map

FileDownload / File: emd_13205.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map, sharpened
Voxel sizeX=Y=Z: 0.84 Å
Density
Contour LevelBy AUTHOR: 0.35 / Movie #1: 0.35
Minimum - Maximum-2.122104 - 3.0768912
Average (Standard dev.)0.0033286337 (±0.0842918)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.840.840.84
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-2.1223.0770.003

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Supplemental data

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Mask #1

Fileemd_13205_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: full map, unsharpened

Fileemd_13205_additional_1.map
Annotationfull map, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13205_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13205_half_map_2.map
Projections & Slices
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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 alphaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit betaPolymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'Polymerase
    • Protein or peptide: DNA-directed RNA polymerase subunit omegaPolymerase
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: RNA polymerase-binding protein RbpA
    • DNA: recA-op non-template strand
    • DNA: recA-op template strand
    • Protein or peptide: PafC
    • Protein or peptide: Transcriptional regulator-like protein
  • Ligand: ZINC ION

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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: #1-#10

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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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 37.959441 KDa
SequenceString: MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY ...String:
MLISQRPTLS EETVAENRSR FVIEPLEPGF GYTLGNSLRR TLLSSIPGAA VTSIRIDGVL HEFTTVPGVK EDVTDIILNL KGLVVSSDD DEPVTMYLRK QGPGVVTAGD IVPPAGVTVH NPDMHIATLN DKGKLEVELV VERGRGYVPA VQNKASGAEI G RIPVDSIY SPVLKVTYKV EATRVEQRTD FDKLIIDVET KNSISPRDAL ASAGGTLVEL FGLARELNAD SEHIEIGPSP AE ADHIASF ALPIDDLDLT VRSYNCLKRE GVHTVGELVA RTESDLLDIR NFGQKSIDEV KIKLHQLGLS LKDSPATFDP SEV AGYDAA TGTWTSDAGY DLDDNQDYAE TEQL

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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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 128.680141 KDa
SequenceString: MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS ...String:
MLEGCILAVS SQSKSNAITN NSVPGAPNRV SFAKLREPLE VPGLLDVQTD SFEWLVGSDR WRQAAIDRGE ENPVGGLEEV LAELSPIED FSGSMSLSFS DPRFDEVKAS VDECKDKDMT YAAPLFVTAE FINNNTGEIK SQTVFMGDFP MMTEKGTFII N GTERVVVS QLVRSPGVYF DETIDKSTEK TLHSVKVIPG RGAWLEFDVD KRDTVGVRID RKRRQPVTVL LKALGWTNEQ IV ERFGFSE IMMGTLEKDT TSGTDEALLD IYRKLRPGEP PTKESAQTLL ENLFFKEKRY DLARVGRYKV NKKLGLNAGK PIT SSTLTE EDVVATIEYL VRLHEGQTSM TVPGGVEVPV EVDDIDHFGN RRLRTVGELI QNQIRVGLSR MERVVRERMT TQDV EAITP QTLINIRPVV AAIKEFFGTS QLSQFMDQNN PLSGLTHKRR LSALGPGGLS RERAGLEVRD VHPSHYGRMC PIETP EGPN IGLIGSLSVY ARVNPFGFIE TPYRKVENGV VTDQIDYLTA DEEDRHVVAQ ANSPTDENGR FTEDRVMVRK KGGEVE FVS ADQVDYMDVS PRQMVSVATA MIPFLEHDDA NRALMGANMQ RQAVPLVRSE APLVGTGMEL RAAIDAGDVV VADKTGV IE EVSADYITVM ADDGTRQSYR LRKFARSNHG TCANQRPIVD AGQRVEAGQV IADGPCTQNG EMALGKNLLV AIMPWEGH N YEDAIILSNR LVEEDVLTSI HIEEHEIDAR DTKLGAEEIT RDIPNVSDEV LADLDERGIV RIGAEVRDGD ILVGKVTPK GETELTPEER LLRAIFGEKA REVRDTSLKV PHGESGKVIG IRVFSREDDD ELPAGVNELV RVYVAQKRKI SDGDKLAGRH GNKGVIGKI LPVEDMPFLP DGTPVDIILN THGVPRRMNI GQILETHLGW VAKAGWNIDV AAGVPDWASK LPEELYSAPA D STVATPVF DGAQEGELAG LLGSTLPNRD GEVMVDADGK STLFDGRSGE PFPYPVTVGY MYILKLHHLV DDKIHARSTG PY SMITQQP LGGKAQFGGQ RFGEMECWAM QAYGAAYTLQ ELLTIKSDDT VGRVKVYEAI VKGENIPEPG IPESFKVLLK ELQ SLCLNV EVLSSDGAAI EMRDGDDEDL ERAAANLGIN LSRNESASVE DLA

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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
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 146.712891 KDa
SequenceString: MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA ...String:
MLDVNFFDEL RIGLATADDI RNWSYGEVKK PETINYRTLK PEKDGLFCEK IFGPTRDWEC YCGKYKRVRF KGIICERCGV EVTRAKVRR ERMGHIELAA PVTHIWYFKG VPSRLGYLLD LAPKDLEKII YFAAYVITSV DDEMRHNELS TLEAEMAVEK K AVEDQRDA DLEARAQKLE ADLAELEAEG AKSDVRRKVR DSGEREMRQL RDRAQRELDR LDEIWNTFTK LAPKQLIVDE VL YRELQDR YGEYFTGAMG AESIKKLIEN FDIDAEAESL REVIRSGKGQ KKLRALKRLK VVAAFQQSGN SPMGMVLDAV PVI PPELRP MVQLDGGRFA TSDLNDLYRR VINRNNRLKR LIDLGAPEII VNNEKRMLQE SVDALFDNGR RGRPVTGPGN RPLK SLSDL LKGKQGRFRQ NLLGKRVDYS GRSVIVVGPQ LKLHQCGLPK LMALELFKPF VMKRLVDLNH AQNIKSAKRM VERQR PQVW DVLEEVIAEH PVLLNRAPTL HRLGIQAFEP QLVEGKAIQL HPLVCEAFNA DFDGDQMAVH LPLSAEAQAE ARILML SSN NILSPASGKP LAMPRLDMVT GLYYLTTLVE GATGEYQAAT KDAPEQGVYS SPAEAIMAMD RGALSVRAKI KVRLTEL RP PTDLEAQLFE NGWKPGDAWT AETTLGRVMF NELLPKSYPF VNEQMHKKVQ ARIINDLAER FPMIVVAQTV DKLKDAGF Y WATRSGVTVS MADVLVPPQK QEILERHEAE ADAIERKYQR GALNHTERNE SLVKIWQDAT EEVGKALEEF YPADNPIIT IVKSGATGNL TQTRTLAGMK GLVTNPKGEF IPRPIKSSFR EGLTVLEYFI NTHGARKGLA DTALRTADSG YLTRRLVDVS QDVIVREHD CETERGINVT LAERGPDGTL IRDAHVETSA FARTLATDAV DANGNVIIER GHDLGDPAID ALLAAGITTV K VRSVLTCT SATGVCAMCY GRSMATGKLV DIGEAVGIVA AQSIGEPGTQ LTMRTFHQGG VTGGADIVGG LPRVQELFEA RV PRNKAPI ADVAGRVRLE ESDKFFKITI VPDDGGEEVV YDKLSKRQRL RVITHEDGTE GVLSDGDHVE VGDQLMEGAA DPH EVLRVQ GPREVQIHLV KEVQEVYRAQ GVSIHDKHIE VIVRQMLRRV TIIDSGSTEF LPGSLTERAE FEAENRRVVA EGGE PAAGR PVLMGITKAS LATDSWLSAA SFQETTRVLT DAAINCRSDK LNGLKENVII GKLIPAGTGI SRYRNIQVQP TEEAR AAAY TIPSYEDQYY SPDFGQATGA AVPLDDYGYS DYR

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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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 11.544763 KDa
SequenceString:
MSTPHADAQL NAADDLGIDS SAASAYDTPL GITNPPIDEL LSRASSKYAL VIYAAKRARQ INDYYNQLGD GILEYVGPLV EPGLQEKPL SIALREIHGD LLEHTEGE

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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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 51.573551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTD LELDDLDSDD DTAVEDEEEE ADAATPAVAT AKAADDDIDE PSEKDKASGD FVWDEEESEA LRQARKDAEL T ASADSVRA ...String:
MAATKASPAT EEPVKRTATK TPAKKAPAKR AAKSAAAKAG GKAPAKKAPA KRAAKGTAAK PEDGVTDDLE VTDDLEAEPG EDLDVEDTD LELDDLDSDD DTAVEDEEEE ADAATPAVAT AKAADDDIDE PSEKDKASGD FVWDEEESEA LRQARKDAEL T ASADSVRA YLKQIGKVAL LNAEEEVELA KRIEAGLYAT QKLAELAEKG EKLPVQQRRD MQWICRDGDR AKNHLLEANL RL VVSLAKR YTGRGMAFLD LIQEGNLGLI RAVEKFDYTK GYKFSTYATW WIRQAITRAM ADQARTIRIP VHMVEVINKL GRI QRELLQ DLGREPTPEE LAKEMDITPE KVLEIQQYAR EPISLDQTIG DEGDSQLGDF IEDSEAVVAV DAVSFTLLQD QLQS VLETL SEREAGVVRL RFGLTDGQPR TLDEIGQVYG VTRERIRQIE SKTMSKLRHP SRSQVLRDYL D

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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: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 13.078731 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADRVLRGSR LGAVSYETDR NHDLAPRQVA RYRTDNGEEF DVPFADDAEI PGTWLCRNGL EGTLIEGDVP EPKKVKPPRT HWDMLLERR SVEELEELLK ERLDLIKAKR RGTGS

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Macromolecule #9: PafC

MacromoleculeName: PafC / type: protein_or_peptide / ID: 9 / Details: residues 82-123 have been modelled as poly-alanine / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 34.044402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQVSTRLVR LLNMVPYFQA NPKVTRAEAA AALGVTGKQL DADLDQLWMC GLPGYSPGDL IDFDFVGDTI EVTFSAGVDH PLRLTSTEA TGILVALRAL VDVPGMVDPE AARSAIAKIE SAVGSQRAVV EGITEDTSAE PGAAATVRTA VRENRALTLE Y YSASRDSL ...String:
MSQVSTRLVR LLNMVPYFQA NPKVTRAEAA AALGVTGKQL DADLDQLWMC GLPGYSPGDL IDFDFVGDTI EVTFSAGVDH PLRLTSTEA TGILVALRAL VDVPGMVDPE AARSAIAKIE SAVGSQRAVV EGITEDTSAE PGAAATVRTA VRENRALTLE Y YSASRDSL ATRTVDPIRV VLVGDNSYLE AWCRSAEAVR LFRFDRIVDA QLLDDPAAPP PPAVAAGPDT SLFDADPSLP SA TLLIGAA AAWMFDYYPL RDITERPDGS CEATMTYASE DWMARFILGF GAEVQVLAPE SLATRVRQAA EAALQAYARC V

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Macromolecule #10: Transcriptional regulator-like protein

MacromoleculeName: Transcriptional regulator-like protein / type: protein_or_peptide / ID: 10 / Details: residues 84-128 have been modelled as poly-alanine / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 36.081465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAVSKVERLM NLVIALLSTR TYLPAEKIRT TVAGYADSPS DEAFSRMFER DKNELRDLGI PLETGRVSKW DSTEGYRINR DSYALPPIG LTADEAAAVA VATQLWQSPE LVTATQNAVL KLRAAGVDVD ADGVGVAIAS TATLPGVRGS EEVLQSLLSA I DEGRAVQF ...String:
MAVSKVERLM NLVIALLSTR TYLPAEKIRT TVAGYADSPS DEAFSRMFER DKNELRDLGI PLETGRVSKW DSTEGYRINR DSYALPPIG LTADEAAAVA VATQLWQSPE LVTATQNAVL KLRAAGVDVD ADGVGVAIAS TATLPGVRGS EEVLQSLLSA I DEGRAVQF EHRPSRSADY TTRTVEPWGV VTHRGRWYLV GHDRDREDTR TFRLSRISAA ARPIGPAGAV QKPQDVNLRD IV RRAVAEQ PTGERARIWI AGGRATALRR QAVTSTPRTI GGRAGEEITV DIGTWDRLAR EIASYGSDAV ALEPSSLRDD VVE RLRAHA AGGER

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Macromolecule #7: recA-op non-template strand

MacromoleculeName: recA-op non-template strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 23.733148 KDa
SequenceString: (DT)(DC)(DG)(DT)(DC)(DT)(DA)(DC)(DT)(DG) (DT)(DG)(DG)(DT)(DG)(DA)(DA)(DG)(DA)(DG) (DT)(DT)(DC)(DG)(DA)(DC)(DC)(DG)(DG) (DA)(DC)(DT)(DT)(DG)(DT)(DC)(DG)(DG)(DT) (DG) (DG)(DT)(DC)(DT)(DG)(DC) ...String:
(DT)(DC)(DG)(DT)(DC)(DT)(DA)(DC)(DT)(DG) (DT)(DG)(DG)(DT)(DG)(DA)(DA)(DG)(DA)(DG) (DT)(DT)(DC)(DG)(DA)(DC)(DC)(DG)(DG) (DA)(DC)(DT)(DT)(DG)(DT)(DC)(DG)(DG)(DT) (DG) (DG)(DT)(DC)(DT)(DG)(DC)(DT)(DC) (DT)(DA)(DA)(DC)(DG)(DT)(DC)(DA)(DC)(DG) (DG)(DC) (DC)(DA)(DA)(DC)(DC)(DG)(DA) (DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA)(DC)(DC)

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Macromolecule #8: recA-op template strand

MacromoleculeName: recA-op template strand / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 23.746215 KDa
SequenceString: (DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC)(DG)(DA) (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG) (DA)(DC)(DA)(DT)(DG)(DT)(DA)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DG)(DA)(DC)(DC)(DA) (DC) (DC)(DG)(DA)(DC)(DA)(DA) ...String:
(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC)(DG)(DA) (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DG) (DA)(DC)(DA)(DT)(DG)(DT)(DA)(DA)(DA) (DG)(DA)(DG)(DC)(DA)(DG)(DA)(DC)(DC)(DA) (DC) (DC)(DG)(DA)(DC)(DA)(DA)(DG)(DT) (DC)(DC)(DG)(DG)(DT)(DC)(DG)(DA)(DA)(DC) (DT)(DC) (DT)(DT)(DC)(DA)(DC)(DC)(DA) (DC)(DA)(DG)(DT)(DA)(DG)(DA)(DC)(DG)(DA)

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / 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: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128190

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