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- EMDB-54012: Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bo... -

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Basic information

Entry
Database: EMDB / ID: EMD-54012
TitleStructure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter
Map dataPhiKZ nvRNAP bound to promoter analogue - RELION gold-standard map
Sample
  • Complex: PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L
    • Protein or peptide: DNA-directed RNA polymerase,PHIKZ056.1
    • Protein or peptide: PHIKZ068
    • Protein or peptide: PHIKZ071
    • Protein or peptide: PHIKZ074
    • Protein or peptide: PHIKZ123
    • DNA: DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG
    • DNA: DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT
  • Ligand: ZINC ION
KeywordsPhiKZ / nvRNAP / RNA / DNA / transcription / RNA BINDING PROTEIN
Function / homologyDNA-directed RNA polymerase / PHIKZ056.1 / PHIKZ123 / PHIKZ074 / PHIKZ068
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus) / Phikzvirus phiKZ
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsChen C / de Martin Garrido N / Yakunina M / Aylett CHS
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust206212/Z/17/A United Kingdom
Royal Society206212/Z/17/A United Kingdom
CitationJournal: IUCrJ / Year: 2026
Title: Structure of the bacteriophage PhiKZ non-virion RNA polymerase bound to a p119L open promoter analogue.
Authors: Chao Sheng Chen / Natàlia de Martín Garrido / Maria Yakunina / Christopher H S Aylett /
Abstract: Bacteriophage ΦKZ (PhiKZ) was the first identified member of a family of massive bacterial viruses. ΦKZ infects Pseudomonas aeruginosa, which kills tens of thousands every year, and it therefore ...Bacteriophage ΦKZ (PhiKZ) was the first identified member of a family of massive bacterial viruses. ΦKZ infects Pseudomonas aeruginosa, which kills tens of thousands every year, and it therefore has potential as a bacteriophage therapy. On infection, ΦKZ forms a `nucleus' to protect its genome by excluding host immune systems. This barrier means that it has had to become independent of the host transcriptional apparatus; it cannot simply recruit the host RNA polymerase (RNAP) to its promoters as it is excluded from the viral DNA, and therefore it expresses and imports its own non-virion RNA polymerase (nvRNAP). The ΦKZ nvRNAP, and related jumbo-phage RNAPs including that from bacteriophage AR9, are particularly noteworthy. Unlike typical viral RNAPs which are formed as only a single subunit, it is a non-canonical multi-subunit RNAP directly related to those from eubacteria, and more distantly eukaryotes and archaea. It encompasses four proteins representing patchwork homologues of the eubacterial β/β' subunits, and a fifth that appears to have evolved from a σ factor, but no homologues of the α or ω subunits required for formation of a catalytically active complex in eubacterial RNAPs. Its mechanism of promoter recognition is also highly divergent; transcription is initiated from a site marked only by a tiny four-base consensus sequence co-located with the start site. We have resolved the structure of the ΦKZ nvRNAP bound to an open analogue of its cognate promoter, p119L, revealing that while the σ-factor-like subunit GP68 is involved in bubble stabilization, the sequence-specific promoter consensus sequence is bound between the lobe of the β-subunit homologue GP123 and the enzymatic core of the complex. Our results shed light on the differences between mechanisms of promoter recognition in the ΦKZ nvRNAP and canonical eubacterial RNAPs, and on the uniquely specialized features of bacteriophage transcriptional apparatuses in general.
History
DepositionJun 12, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54012.png

Downloads & links

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Map

FileDownload / File: emd_54012.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhiKZ nvRNAP bound to promoter analogue - RELION gold-standard map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 288 pix.
= 285.12 Å		0.99 Å/pix.
x 288 pix.
= 285.12 Å		0.99 Å/pix.
x 288 pix.
= 285.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.01718076 - 0.059539188
Average (Standard dev.)0.00026025833 (±0.0023362704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 285.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54012_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: PhiKZ nvRNAP bound to promoter analogue - sharpened 2.5A map

Fileemd_54012_additional_1.map
AnnotationPhiKZ nvRNAP bound to promoter analogue - sharpened 2.5A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PhiKZ nvRNAP bound to promoter analogue - RELION...

Fileemd_54012_half_map_1.map
AnnotationPhiKZ nvRNAP bound to promoter analogue - RELION gold-standard half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PhiKZ nvRNAP bound to promoter analogue - RELION...

Fileemd_54012_half_map_2.map
AnnotationPhiKZ nvRNAP bound to promoter analogue - RELION gold-standard half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L

EntireName: PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L
Components
  • Complex: PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L
    • Protein or peptide: DNA-directed RNA polymerase,PHIKZ056.1
    • Protein or peptide: PHIKZ068
    • Protein or peptide: PHIKZ071
    • Protein or peptide: PHIKZ074
    • Protein or peptide: PHIKZ123
    • DNA: DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG
    • DNA: DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT
  • Ligand: ZINC ION

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Supramolecule #1: PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L

SupramoleculeName: PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Details: Mismatches introduced around the transcription start site to stably open the bubble
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: DNA-directed RNA polymerase,PHIKZ056.1

MacromoleculeName: DNA-directed RNA polymerase,PHIKZ056.1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 57.976605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MGLYAKVVDH NEVHDQFTGK RIYANDYNTS NSDEKEEFDR HFYSHFQDSE AIESSVSCDC RAIEDAHKL GVICDICNTP VVNTSSRPIE PSMWVRTPKH VRSLINPRLI IMLTGYLVTK EFDFLAYLTD TSYRYDVESI G SKETRRKV ...String:
MGSSHHHHHH SSGLVPRGSH MGLYAKVVDH NEVHDQFTGK RIYANDYNTS NSDEKEEFDR HFYSHFQDSE AIESSVSCDC RAIEDAHKL GVICDICNTP VVNTSSRPIE PSMWVRTPKH VRSLINPRLI IMLTGYLVTK EFDFLAYLTD TSYRYDVESI G SKETRRKV DRLLHRGFER GLNHFIDNFN EIFQFLLDAN IISNNKSEFA QFVAQNKDKL FPKYLPVPSK LCFVAESTTS GT YLDKPIE AAIDATLTFA SIDASSVPLS PIKAQNRTMR GLRLYGQFYE IYAKSRIAQK PGLARRHMFG ARLNATARAV ITS ISDPHD YDELHIPWGV GCQLLKYHLT NKLKAKFNMT TREAFSFVYE NVLQYNQIIA DLFKELIAEA APYKGMGCTF HRNP TLQRG STQQFFITKV KDDINDNSIS MSVLCLKAPN ADFDGDQLNL TLMPDVYLTK ATERIAPHTW VLSIDEPHEI SGNLE LQGP VVETIINWAH EKYLPPLEEW LKAK

UniProtKB: DNA-directed RNA polymerase, PHIKZ056.1

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Macromolecule #2: PHIKZ068

MacromoleculeName: PHIKZ068 / type: protein_or_peptide / ID: 2 / Details: Numbering correct in original mmCIF file / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 59.442824 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEIIVTGVQG TGFTEVATEH NGKRLTWTTT AYSKIRVQDQ QRVFQEINDY WSGLSAEAQQ HIWNCYVEIR KIMDMAMHPM RIAMSLSYY IKEMYKAMPM NSFRRWLLTI GKLYIPVDIE EVITDDSRYN RPDQTYLKHD YINLASVSLA LRPLVPIWGE F IDQGTSQE ...String:
MEIIVTGVQG TGFTEVATEH NGKRLTWTTT AYSKIRVQDQ QRVFQEINDY WSGLSAEAQQ HIWNCYVEIR KIMDMAMHPM RIAMSLSYY IKEMYKAMPM NSFRRWLLTI GKLYIPVDIE EVITDDSRYN RPDQTYLKHD YINLASVSLA LRPLVPIWGE F IDQGTSQE MHKECEVISL ISDCEVNHWP VDEISIDGTP VETAYDKLSA YVKFCVEDEA PTLANLYRGM SSAEVPDILQ AK VMVRRLT ILPLNDATSH SIVSNMFRYV KSNLNPAERS TADRVNDKRP DKGGIDDDDK TSFIESHKTK QRVTPGDIVA YNL DALDVV KLVHKIDDTV PVELIQECLD CVAVTATKDI YPHQILLAQW VMHKAFPARA FSHINKNAVN HLLAAAQSLM WHWG FQQVA VFMQVELYYS GEHAMSIQPR NSTRIQIKYK DVMDELYPHQ RQQRAINGVP VAPVNIAGIA VQSAHASIRS SNWIY HGPD RLFKEAEQVT QNKVLVVPAT IKSVITELVI HLGKLNQ

UniProtKB: PHIKZ068

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Macromolecule #3: PHIKZ071

MacromoleculeName: PHIKZ071 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 78.780453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSQLGRREID LTLLGHTGLD PWYGTTSSAR GAMFVTHIGQ APEVNGNESR YFLTGAELEY AKYTHDVRFP EDCRVLHVLR KYPTGIGKD SIRSNPVTTI IYENYFDKYK TIGVLHVPEY MSHHQDFGYE LVKNREVWET IAPNEMFSKD TVIAQSGAVK K DGTLGMGV ...String:
MSQLGRREID LTLLGHTGLD PWYGTTSSAR GAMFVTHIGQ APEVNGNESR YFLTGAELEY AKYTHDVRFP EDCRVLHVLR KYPTGIGKD SIRSNPVTTI IYENYFDKYK TIGVLHVPEY MSHHQDFGYE LVKNREVWET IAPNEMFSKD TVIAQSGAVK K DGTLGMGV NANVVFLSAA GTIEDGFVAN KNFLKRMMPT SYSTAVANAG RKAFFLNMYG DDKIYKPFPD IGDVIRPDGV IF AIRDHDD DLAPAEMTPR ALRTLDRTFD RAVIGTPGAK VIDIDIWRDE RVNPSPTPTG MDAQLVKYHT HLSSYYRELL KIY RGLLAR RKDDLHITEE FERLIVTAQM FLPQPDNVRK LSRFYRLDPL DEWRVEVTYK AQKMPAGAFK MTDFHGGKGV ICKV MEDED MPIDENGNRA DLIIFGGSTM RRSNYGRIYE HGFGAAARDL AQRLRVEAGL DRHAKPTQQQ LNSVMGNTQW VDYAF KELL GFYEIIAPTM HSKMMEHPNP AEHVKTVLMD GFPYIYAPVD DPVDLMAAVN KLINSDKYRP HYGKVSYRDQ AGKWVT TKD NVLMGPLYMM LLEKIGEDWS AAASVKTQPF GLPSKLNNAD RASTPGRETA IRSFGESETR SYNCTVGPGP TAEILDQ TN NPLAHAAVIE SWLTAEKPSS VPVAVDREKI PFGGSRPVAM FDHLLECSGI ALEYAPDH

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Macromolecule #4: PHIKZ074

MacromoleculeName: PHIKZ074 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 77.513461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNLNRYKARD LLNLSYDDLW SLPSEWHLIE FDDGKTVVSV DRITKLSVLC WYPLKHYKDC PIPSDHHIDF NRILTDNPKD YLNVEGGRV TSKAMVKHLN KAIWNIYDWS GETVDPEVLS KLAIEGKNWL YNQTTVKLSE YLATLSMFDI AEVYNHPKVR E ANHNIEPT ...String:
MNLNRYKARD LLNLSYDDLW SLPSEWHLIE FDDGKTVVSV DRITKLSVLC WYPLKHYKDC PIPSDHHIDF NRILTDNPKD YLNVEGGRV TSKAMVKHLN KAIWNIYDWS GETVDPEVLS KLAIEGKNWL YNQTTVKLSE YLATLSMFDI AEVYNHPKVR E ANHNIEPT TYGIEKISYG KVKEVFNDPT QFIGNSIIEG LRSGTQKTEQ LLQAFAWRGF PTDINSDIFK YPVTTGYIDG IW NLYENMI ESRSGTKALL YNKELLRVTE YFNRKSQLIA QYVQRLHPGD CKTTILAEYP VTKLTLKAFK GKYYQKEDGK LDW IRGNET HLIGTKQKFR SVFGCNHPDS QGICMTCYGR LGINIPKGTN IGQVAAVSMG DKITSAVLST KHTDASSAVE QYKL GKIES NYLRTGEIPE TLYLKKELTQ KDYRLVIARS EAENLADILM IDDLTAYPAT SATELTSLAL VYDDEVNGEC GDVLT VSLY NRRASLSIEM LKHIKMVRWE LDQRDNIVIS LRGFDFNLPF LTLPNKHVNM YEVMKRFQSF LHSGSDSAEA GKLSTE KVG YTSKTYLKNY KSPIEALPVF ATMANEKISL NISHCEILIY AMMIRSAQYR DYRLPKPGIN GQFEKYNRLM QCRSLGG AM AFEKQHEPLN NPGSFLNKMR NDHPYDLLVK GGKLR

UniProtKB: PHIKZ074

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Macromolecule #5: PHIKZ123

MacromoleculeName: PHIKZ123 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 62.95909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPDPFLIEKI RENTPCMNPT LANGITVEHT MTRDPNTGVN MTRRYIDSLF DISSVLFPDG FKYEGNRACT PLKHFEEITR EYNAKRIAN IAPTDMYMID LMFSYKGEML YPRPMLLPAF KRGNMVTING AKYIGSPVLT DVGFSVLNDS IFIPFRRTKL T FKQTDHHY ...String:
MPDPFLIEKI RENTPCMNPT LANGITVEHT MTRDPNTGVN MTRRYIDSLF DISSVLFPDG FKYEGNRACT PLKHFEEITR EYNAKRIAN IAPTDMYMID LMFSYKGEML YPRPMLLPAF KRGNMVTING AKYIGSPVLT DVGFSVLNDS IFIPFRRTKL T FKQTDHHY MCNGQRKIMY VIWSQIHNEM AKRTKRDLGN RPHIESCLAH YFFCQFGVTQ TFKQWANVDV KCGLLSDFPE EE YPREKWN IYSSATLKGK HPTGEMVLVI PRHQESIFAT RLIAGFWYVV DAFPMRFTRP EYVDSTNLWR VILGHMVFGD FEH QGKVEE NIDSHLHSFC NSLDEMTIEE LKTVGVNVST IWELLYEIMT SLAHHLYATD IDETSMYGKR LTVLHYLMSE FNYA VSMFG YMFQSRRDRE WTVQELNEGL KRSFKLQTAI KRLTVDHGEL DTMSNPNSSM LIKGTSILVT QDRAKTAKAH NKSLI NDSS RIIHASIAEV GQYKNQPKNN PDGRGRLNMY TKVGPTGLVE RREEVREIID NAQLMFRAK

UniProtKB: PHIKZ123

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Macromolecule #6: DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCT...

MacromoleculeName: DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 23.218951 KDa
SequenceString: (DA)(DT)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DT) (DT)(DT)(DA)(DG)(DT)(DG)(DA)(DA)(DT)(DG) (DT)(DA)(DT)(DT)(DT)(DG)(DC)(DT)(DA) (DT)(DA)(DT)(DT)(DG)(DC)(DT)(DA)(DT)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG) ...String:
(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DT) (DT)(DT)(DA)(DG)(DT)(DG)(DA)(DA)(DT)(DG) (DT)(DA)(DT)(DT)(DT)(DG)(DC)(DT)(DA) (DT)(DA)(DT)(DT)(DG)(DC)(DT)(DA)(DT)(DG) (DT) (DA)(DG)(DA)(DC)(DA)(DG)(DT)(DT) (DC)(DC)(DC)(DA)(DA)(DA)(DA)(DG)(DC)(DC) (DT)(DA) (DA)(DA)(DG)(DT)(DT)(DA)(DC) (DA)(DA)(DT)(DA)(DT)(DA)(DG)(DG)

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Macromolecule #7: DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATT...

MacromoleculeName: DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT
type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Phikzvirus phiKZ
Molecular weightTheoretical: 22.881719 KDa
SequenceString: (DC)(DC)(DT)(DA)(DT)(DA)(DT)(DT)(DG)(DT) (DA)(DA)(DC)(DT)(DT)(DT)(DA)(DG)(DG)(DC) (DT)(DT)(DT)(DT)(DG)(DG)(DG)(DA)(DA) (DC)(DT)(DC)(DC)(DT)(DC)(DT)(DC)(DA)(DT) (DA) (DT)(DT)(DC)(DC)(DC)(DA) ...String:
(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DT)(DG)(DT) (DA)(DA)(DC)(DT)(DT)(DT)(DA)(DG)(DG)(DC) (DT)(DT)(DT)(DT)(DG)(DG)(DG)(DA)(DA) (DC)(DT)(DC)(DC)(DT)(DC)(DT)(DC)(DA)(DT) (DA) (DT)(DT)(DC)(DC)(DC)(DA)(DT)(DA) (DG)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA)(DT) (DT)(DC) (DA)(DC)(DT)(DA)(DA)(DA)(DA) (DT)(DT)(DA)(DC)(DT)(DC)(DA)(DT)

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
40.0 mMTris-ClTris-Cl
10.0 mMMgCl2MgCl2
5.0 mMDTTDTT
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
Details: Settings: -4 blot force, 4 s waiting time and 0.5-1 s blotting time..
DetailsPhiKZ nvRNAP complexes were mixed at 0.1 mg/mL final concentration with the P119L promoter analogue at a 1:1 ratio. Reactions were incubated for 30 min at 25 C before use.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 20670 / Average electron dose: 50.0 e/Å2 / Details: Images collected as TIFF movies
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 4178816
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Prior map from 7OGP study
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 329400
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 128002 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
chain_id: B, residue_range: 0-278, source_name: AlphaFold, initial_model_type: in silico model
chain_id: X, source_name: Other, initial_model_type: in silico modelIdealised B-DNA
chain_id: Y, source_name: Other, initial_model_type: in silico modelIdealised B-DNA
source_name: PDB, initial_model_type: experimental model

7ogp

source_name: PDB, initial_model_type: experimental model

7ogr

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 104.82 / Target criteria: CC
Output model

PDB-9rjs:
Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter

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