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

2026-04-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2025-06-12 2025-07-16 2025-07-16 2026-04-01 Wellcome Trust 206212/Z/17/A United Kingdom Royal Society 206212/Z/17/A United Kingdom Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter Chen C de Martin Garrido N Yakunina M Aylett CHS PhiKZ, nvRNAP, RNA, DNA, transcription, RNA BINDING PROTEIN Chen CS de Martin Garrido N Yakunina M Aylett CHS Structure of the bacteriophage PhiKZ non-virion RNA polymerase bound to a p119L open promoter analogue. Iucrj UK 13 31 43 2026 41212033 doi:10.1107/S2052252525009273 2052-2525 9rjs FULLOVERLAP PDB 7OGP unspecified

Previous structure of core

PDB 7OGR unspecified

Previous structure of core

PDB 8QUE unspecified

Previous structure with DNA and RNA

EMDB EMD-54012 associated EM volume

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

PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L PhiKZ non-virion RNA polymerase bound to an analogue of promoter p119L 0 1 2 3 4 5 6 7

Mismatches introduced around the transcription start site to stably open the bubble

Pseudomonas phage phiKZ 0.4 DNA-directed RNA polymerase,PHIKZ056.1 Phikzvirus phiKZ 0.057976605 1 Escherichia coli LEVO MGSSHHHHHHSSGLVPRGSHMGLYAKVVDHNEVHDQFTGKRIYANDYNTSNSDEKEEFDRHFYSHFQDSEAIESSVSCDC RAIEDAHKLGVICDICNTPVVNTSSRPIEPSMWVRTPKHVRSLINPRLIIMLTGYLVTKEFDFLAYLTDTSYRYDVESIG SKETRRKVDRLLHRGFERGLNHFIDNFNEIFQFLLDANIISNNKSEFAQFVAQNKDKLFPKYLPVPSKLCFVAESTTSGT YLDKPIEAAIDATLTFASIDASSVPLSPIKAQNRTMRGLRLYGQFYEIYAKSRIAQKPGLARRHMFGARLNATARAVITS ISDPHDYDELHIPWGVGCQLLKYHLTNKLKAKFNMTTREAFSFVYENVLQYNQIIADLFKELIAEAAPYKGMGCTFHRNP TLQRGSTQQFFITKVKDDINDNSISMSVLCLKAPNADFDGDQLNLTLMPDVYLTKATERIAPHTWVLSIDEPHEISGNLE LQGPVVETIINWAHEKYLPPLEEWLKAK I7DB47 L7T138 PHIKZ068 Phikzvirus phiKZ 0.059442824

Numbering correct in original mmCIF file

1 Escherichia coli LEVO MEIIVTGVQGTGFTEVATEHNGKRLTWTTTAYSKIRVQDQQRVFQEINDYWSGLSAEAQQHIWNCYVEIRKIMDMAMHPM RIAMSLSYYIKEMYKAMPMNSFRRWLLTIGKLYIPVDIEEVITDDSRYNRPDQTYLKHDYINLASVSLALRPLVPIWGEF IDQGTSQEMHKECEVISLISDCEVNHWPVDEISIDGTPVETAYDKLSAYVKFCVEDEAPTLANLYRGMSSAEVPDILQAK VMVRRLTILPLNDATSHSIVSNMFRYVKSNLNPAERSTADRVNDKRPDKGGIDDDDKTSFIESHKTKQRVTPGDIVAYNL DALDVVKLVHKIDDTVPVELIQECLDCVAVTATKDIYPHQILLAQWVMHKAFPARAFSHINKNAVNHLLAAAQSLMWHWG FQQVAVFMQVELYYSGEHAMSIQPRNSTRIQIKYKDVMDELYPHQRQQRAINGVPVAPVNIAGIAVQSAHASIRSSNWIY HGPDRLFKEAEQVTQNKVLVVPATIKSVITELVIHLGKLNQ Q8SD94 PHIKZ071 Phikzvirus phiKZ 0.07878045299999999 1 Escherichia coli LEVO MSQLGRREIDLTLLGHTGLDPWYGTTSSARGAMFVTHIGQAPEVNGNESRYFLTGAELEYAKYTHDVRFPEDCRVLHVLR KYPTGIGKDSIRSNPVTTIIYENYFDKYKTIGVLHVPEYMSHHQDFGYELVKNREVWETIAPNEMFSKDTVIAQSGAVKK DGTLGMGVNANVVFLSAAGTIEDGFVANKNFLKRMMPTSYSTAVANAGRKAFFLNMYGDDKIYKPFPDIGDVIRPDGVIF AIRDHDDDLAPAEMTPRALRTLDRTFDRAVIGTPGAKVIDIDIWRDERVNPSPTPTGMDAQLVKYHTHLSSYYRELLKIY RGLLARRKDDLHITEEFERLIVTAQMFLPQPDNVRKLSRFYRLDPLDEWRVEVTYKAQKMPAGAFKMTDFHGGKGVICKV MEDEDMPIDENGNRADLIIFGGSTMRRSNYGRIYEHGFGAAARDLAQRLRVEAGLDRHAKPTQQQLNSVMGNTQWVDYAF KELLGFYEIIAPTMHSKMMEHPNPAEHVKTVLMDGFPYIYAPVDDPVDLMAAVNKLINSDKYRPHYGKVSYRDQAGKWVT TKDNVLMGPLYMMLLEKIGEDWSAAASVKTQPFGLPSKLNNADRASTPGRETAIRSFGESETRSYNCTVGPGPTAEILDQ TNNPLAHAAVIESWLTAEKPSSVPVAVDREKIPFGGSRPVAMFDHLLECSGIALEYAPDH PHIKZ074 Phikzvirus phiKZ 0.07751346099999999 1 Escherichia coli LEVO MNLNRYKARDLLNLSYDDLWSLPSEWHLIEFDDGKTVVSVDRITKLSVLCWYPLKHYKDCPIPSDHHIDFNRILTDNPKD YLNVEGGRVTSKAMVKHLNKAIWNIYDWSGETVDPEVLSKLAIEGKNWLYNQTTVKLSEYLATLSMFDIAEVYNHPKVRE ANHNIEPTTYGIEKISYGKVKEVFNDPTQFIGNSIIEGLRSGTQKTEQLLQAFAWRGFPTDINSDIFKYPVTTGYIDGIW NLYENMIESRSGTKALLYNKELLRVTEYFNRKSQLIAQYVQRLHPGDCKTTILAEYPVTKLTLKAFKGKYYQKEDGKLDW IRGNETHLIGTKQKFRSVFGCNHPDSQGICMTCYGRLGINIPKGTNIGQVAAVSMGDKITSAVLSTKHTDASSAVEQYKL GKIESNYLRTGEIPETLYLKKELTQKDYRLVIARSEAENLADILMIDDLTAYPATSATELTSLALVYDDEVNGECGDVLT VSLYNRRASLSIEMLKHIKMVRWELDQRDNIVISLRGFDFNLPFLTLPNKHVNMYEVMKRFQSFLHSGSDSAEAGKLSTE KVGYTSKTYLKNYKSPIEALPVFATMANEKISLNISHCEILIYAMMIRSAQYRDYRLPKPGINGQFEKYNRLMQCRSLGG AMAFEKQHEPLNNPGSFLNKMRNDHPYDLLVKGGKLR Q8SD88 PHIKZ123 Phikzvirus phiKZ 0.06295909 1 Escherichia coli LEVO MPDPFLIEKIRENTPCMNPTLANGITVEHTMTRDPNTGVNMTRRYIDSLFDISSVLFPDGFKYEGNRACTPLKHFEEITR EYNAKRIANIAPTDMYMIDLMFSYKGEMLYPRPMLLPAFKRGNMVTINGAKYIGSPVLTDVGFSVLNDSIFIPFRRTKLT FKQTDHHYMCNGQRKIMYVIWSQIHNEMAKRTKRDLGNRPHIESCLAHYFFCQFGVTQTFKQWANVDVKCGLLSDFPEEE YPREKWNIYSSATLKGKHPTGEMVLVIPRHQESIFATRLIAGFWYVVDAFPMRFTRPEYVDSTNLWRVILGHMVFGDFEH QGKVEENIDSHLHSFCNSLDEMTIEELKTVGVNVSTIWELLYEIMTSLAHHLYATDIDETSMYGKRLTVLHYLMSEFNYA VSMFGYMFQSRRDREWTVQELNEGLKRSFKLQTAIKRLTVDHGELDTMSNPNSSMLIKGTSILVTQDRAKTAKAHNKSLI NDSSRIIHASIAEVGQYKNQPKNNPDGRGRLNMYTKVGPTGLVERREEVREIIDNAQLMFRAK Q8SD39 DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG Phikzvirus phiKZ 0.023218951 1 (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) DNA DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT Phikzvirus phiKZ 0.022881719 1 (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) DNA ZINC ION 6.5409e-05 2 ZN singleParticle particle 0.1 8.0 40.0 Tris-Cl Tris-Cl 10.0 MgCl2 MgCl2 5.0 DTT DTT Quantifoil R2/1 GOLD 300 GRAPHENE OXIDE CONTINUOUS PLASMA CLEANING 60 AIR ETHANE 100 289 FEI VITROBOT MARK IV

Settings: -4 blot force, 4 s waiting time and 0.5-1 s blotting time..

PhiKZ 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.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.75 2.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 10 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 1 20670 50.0

Images collected as TIFF movies

1 4178816 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Prior map from 7OGP study

1 C1 FOURIER SPACE 2.59 FSC 0.143 CUT-OFF RELION 4 329400 PROJECTION MATCHING RELION 4 PROJECTION MATCHING RELION 4 4 128002.0 RELION 4 emd_54012.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 285.12 285.12 285.12 90.0 90.0 90.0 X Y Z -0.01718076 0.059539188 0.00026025833 0.0023362704 0.99 0.99 0.99 0.016 AUTHOR ::::EMDATABANK.org::::EMD-54012:::: PhiKZ nvRNAP bound to promoter analogue - RELION gold-standard map B 0-278 AlphaFold in silico model X Other in silico model

Idealised B-DNA

Y Other in silico model

Idealised B-DNA

7OGP PDB experimental model 7OGR PDB experimental model AB INITIO MODEL CC REAL 104.819999999999993 emd_54012_msk_1.map emd_54012_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 285.12 285.12 285.12 90.0 90.0 90.0 X Y Z -0.08471603 0.16114883 0.0001785772 0.0059514684 0.99 0.99 0.99 AUTHOR ::::EMDATABANK.org::::EMD-54012:::: PhiKZ nvRNAP bound to promoter analogue - sharpened 2.5A map emd_54012_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 285.12 285.12 285.12 90.0 90.0 90.0 X Y Z -0.02123346 0.067909755 0.00025393 0.0027733825 0.99 0.99 0.99 AUTHOR ::::EMDATABANK.org::::EMD-54012:::: PhiKZ nvRNAP bound to promoter analogue - RELION gold-standard half map 1 emd_54012_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 285.12 285.12 285.12 90.0 90.0 90.0 X Y Z -0.022346133 0.06347251 0.00028071486 0.0027685952 0.99 0.99 0.99 AUTHOR ::::EMDATABANK.org::::EMD-54012:::: PhiKZ nvRNAP bound to promoter analogue - RELION gold-standard half map 2