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- PDB-11go: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (... -

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Basic information

Entry
Database: PDB / ID: 11go
TitleCryo-EM structure of the bacteriophage N4 virion RNA polymerase (transcription initiation complex)
Components
  • DNA (5'-D(P*AP*AP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*T)-3')
  • Virion DNA-directed RNA polymerase
KeywordsVIRAL PROTEIN / N4 Bacteriophage vRNAP
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / virion component / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
: / : / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain / Virion DNA-directed RNA polymerase domain / Bacteriophage N4 RNA polymerase, helical domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsNarwal, M. / Shin, Y. / Murakami, K.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Bacteriol / Year: 2026
Title: Cryo-EM study of bacteriophage N4 virion RNA polymerase.
Authors: Manju Narwal / Yeonoh Shin / Katsuhiko S Murakami /
Abstract: Coliphage N4 employs a unique infection and transcription strategy in which early gene expression is driven by a virion-encapsidated RNA polymerase (vRNAP) that is injected into the host cytoplasm ...Coliphage N4 employs a unique infection and transcription strategy in which early gene expression is driven by a virion-encapsidated RNA polymerase (vRNAP) that is injected into the host cytoplasm upon infection. Despite extensive biochemical and crystallographic studies of the polymerase domain of vRNAP, the structural organization and regulatory roles of the N-terminal domain (NTD) and C-terminal domain (CTD) regions of the 3,500-residue-long whole enzyme have remained unresolved. Here, we report the cryo-electron microscopy (cryo-EM) structures of full-length N4 vRNAP in its apo state and in a transcription initiation complex (TIC) with promoter DNA and initiating nucleotides. The apo structure reveals a modular architecture in which an α-helical CTD packs against the Pol domain to stabilize an autoinhibited conformation characterized by occlusion of the nucleotide-binding site through tight contact between the plug module and motif B loop. In contrast, promoter binding induces conformational rearrangements that displace the motif B loop from the active site and separate the CTD from the Pol domain. The NTD is unresolved in both states, consistent with substantial intrinsic flexibility, and supporting its proposed role in membrane association and genome injection. Structural modeling suggests that domain segmentation and conformational plasticity may enable translocation of vRNAP through the ~30 Å wide phage tail channel during infection. Together, these results define the molecular architecture of full-length vRNAP and establish a structural framework for understanding how the conformational transition of vRNAP is coupled to its ejection, DNA injection, and early gene expression.IMPORTANCEThis study investigates the structure of full-length bacteriophage N4 virion RNA polymerase (vRNAP), one of the largest known single-subunit RNA polymerases. The functions of its extensive N- and C-terminal regions remained unknown. Our work uncovers how the C-terminal domain regulates polymerase activity through a structural "switch" that locks the enzyme in an inactive state until it recognizes its promoter DNA. These findings explain how the phage prevents premature transcription and ensures precise control of early gene expression during infection. By integrating structures with the architecture of the N4 phage particle, we propose a mechanism by which this vRNAP is transported through the narrow phage tail into the host cell. Together, this work provides fundamental insight into phage transcription and viral gene regulation.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion DNA-directed RNA polymerase
C: DNA (5'-D(P*AP*AP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,5785
Polymers373,5072
Non-polymers1,0713
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Virion DNA-directed RNA polymerase / vRNAP / Gene product 50 / gp50


Mass: 359891.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: MSVFDRLAGFADSVTNAKQVDVSTATAQKKAEQGVTTPLVSPDAAYQMQAARTGNVGANAFEPGTVQSDFMNLTPMQIMNKYGVEQGLQLINARADAGNQVFNDSVTTRTPGEELGDIATGVGLGFVNTLGGIGALGAGLLNDDAGAVVAQQLSKFNDAVHATQSQALQDKRKLFAARNLMNEVESERQYQTDKKEGTNDIVASLSKFGRDFVGSIENAAQTDSIISDGLAEGVGSLLGAGPVLRGASLLGKAVVPANTLRSAALAGAIDAGTGTQSLARIASTVGRAAPGMVGVGAMEAGGAYQQTADEIMKMSLKDLEKSPVYQQHIKDGMSPEQARRQTASETGLTAAAIQLPIAAATGPLVSRFEMAPFRAGSLGAVGMNLARETVEEGVQGATGQLAQNIAQQQNIDKNQDLLKGVGTQAGLGALYGFGSAGVVQAPAGAARLAGAATAPVLRTTMAGVKAAGSVAGKVVSPIKNTLVARGERVMKQNEEASPVADDYVAQAAQEAMAQAPEAEVTIRDAVEATDATPEQKVAAHQYVSDLMNATRFNPENYQEAPEHIRNAVAGSTDQVQVIQKLADLVNTLDESNPQALMEAASYMYDAVSEFEQFINRDPAALDSIPKDSPAIELLNRYTNLTANIQNTPKVIGALNVINRMINESAQNGSLNVTEESSPQEMQNVALAAEVAPEKLNPESVNVVLKHAADGRIKLNNRQIAALQNAAAILKGAREYDAEAARLGLRPQDIVSKQIKTDESRTQEGQYSALQHANRIRSAYNSGNFELASAYLNDFMQFAQHMQNKVGALNEHLVTGNADKNKSVHYQALTADREWVRSRTGLGVNPYDTKSVKFAQQVALEAKTVADIANALASAYPELKVSHIKVTPLDSRLNAPAAEVVKAFRQGNRDVASSQPKADSVNQVKETPVTKQEPVTSTVQTKTPVSESVKTEPTTKESSPQAIKEPVNQSEKQDVNLTNEDNIKQPTESVKETETSTKESTVTEELKEGIDAVYPSLVGTADSKAEGIKNYFKLSFTLPEEQKSRTVGSEAPLKDVAQALSSRARYELFTEKETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGTEANRWVGGKLLNIVEQDGDTFKYNEQLLQTAVLAGLQWRLTATSNTAIKDAKDVAAITGIDQALLPEGLVEQFDTGMTLTEAVSSLAQKIESYWGLSRNPNAPLGYTKGIPTAMAAEILAAFVESTDVVENIVDMSEIDPDNKKTIGLYTITELDSFDPINSFPTAIEEAVLVNPTEKMFFGDDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGTLNKELLNDNHAKSLEGKNRSVEDSYNQLFSVIEQVRAQSEDISTVPIHYAYNMTRVGRMQMLGKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLGLAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAEDKSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKLRSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVSSVTDAIYERMSDVLKARAKDPNISAAMAMFGKQAASEAHAEELLARFLKDMETLTSTVPVKRKGVLELQSTGTGAKGKINPKTYTIKGEQLKALQENMLHFFVEPLRNGITQTVGESLVYSTEQLQKATQIQSVVLEDMFKQRVQEKLAEKAKDPTWKKGDFLTQKELNDIQASLNNLAPMIETGSQTFYIAGSENAEVANQVLATNLDDRMRVPMSIYAPAQAGVAGIPFMTIGTGDGMMMQTLSTMKGAPKNTLKIFDGMNIGLNDITDASRKANEAVYTSWQGNPIKNVYESYAKFMKNVDFSKLSPEALEAIGKSALEYDQRENATVDDIANAASLIERNLRNIALGVDIRHKVLDKVNLSIDQMAAVGAPYQNNGKIDLSNMTPEQQADELNKLFREELEARKQKVAKARAEVKEETVSEKEPVNPDFGMVGREHKASGVRILSATAIRNLAKISNLPSTQAATLAEIQKSLAAKDYKIIYGTPTQVAEYARQKNVTELTSQEMEEAQAGNIYGWTNFDDKTIYLVSPSMETLIHELVHASTFEEVYSFYQGNEVSPTSKQAIENLEGLMEQFRSLDISKDSPEMREAYADAIATIEGHLSNGFVDPAISKAAALNEFMAWGLANRALAAKQKRTSSLVQMVKDVYQAIKKLIWGRKQAPALGEDMFSNLLFNSAILMRSQPTTQAVAKDGTLFHSKAYGNNERLSQLNQTFDKLVTDYLRTDPVTEVERRGNVANALMSATRLVRDVQSHGFNMTAQEQSVFQMVTAALATEAAIDPHAMARAQELYTHVMKHLTVEHFMADPDSTNPADRYYAQQKYDTISGANLVEVDAKGRTSLLPTFLGLAMVNEELRSIIKEMPVPKADKKLGNDIDTLLTNAGTQVMESLNRRMAGDQKATNVQDSIDALSETIMAAALKRESFYDAVATPTGNFIDRANQYVTDSIERLSETVIEKADKVIANPSNIAAKGVAHLAKLTAAIASEKQGEIVAQGVMTAMNQGKVWQPFHDLVNDIVGRTKTNANVYDLIKLVKSQISQDRQQFREHLPTVIAGKFSRKLTDTEWSAMHTGLGKTDLAVLRETMSMAEIRDLLSSSKKVKDEISTLEKEIQNQAGRNWNLVQKKSKQLAQYMIMGEVGNNLLRNAHAISRLLGERITNGPVADVAAIDKLITLYSLELMNKSDRDLLSELAQSEVEGMEFSIAYMVGQRTEEMRKAKGDNRTLLNHFKGYIPVENQQGVNLIIADDKEFAKLNSQSFTRIGTYQGSTGFRTGSKGYYFSPVAARAPYSQGILQNVRNTAGGVDIGTGFTLGTMVAGRITDKPTVERITKALAKGERGREPLMPIYNSKGQVVAYEQSVDPNMLKHLNQDNHFAKMVGVWRGRQVEEAKAQRFNDILIEQLHAMYEKDIKDSSANKSQYVNLLGKIDDPVLADAINLMNIETRHKAEELFGKDELWVRRDMLNDALGYRAASIGDVWTGNSRWSPSTLDTVKKMFLGAFGNKAYHVVMNAENTIQNLVKDAKTVIVVKSVVVPAVNFLANIYQMIGRGVPVKDIAVNIPRKTSEINQYIKSRLRQIDAEAELRAAEGNPNLVRKLKTEIQSITDSHRRMSIWPLIEAGEFSSIADAGISRDDLLVAEGKIHEYMEKLANKLPEKVRNAGRYALIAKDTALFQGIQKTVEYSDFIAKAIIYDDLVKRKKKSSSEALGQVTEEFINYDRLPGRFRGYMESMGLMWFYNFKIRSIKVAMSMIRNNPVHSLIATVVPAPTMFGNVGLPIQDNMLTMLAEGRLDYSLGFGQGLRAPTLNPWFNLTH
Source: (gene. exp.) Escherichia phage N4 (virus) / Gene: 50
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q859P9, DNA-directed RNA polymerase
#2: DNA chain DNA (5'-D(P*AP*AP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*T)-3')


Mass: 13615.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Hairpin promoter / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: minivRNAP with the hairpin promoter in a transcribing state
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.1199 MDa / Experimental value: NO
Source (natural)Organism: Escherichia phage N4 (virus)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50000 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
RefinementHighest resolution: 2.82 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069029
ELECTRON MICROSCOPYf_angle_d0.54612338
ELECTRON MICROSCOPYf_dihedral_angle_d16.2881441
ELECTRON MICROSCOPYf_chiral_restr0.0411420
ELECTRON MICROSCOPYf_plane_restr0.0031523

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