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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: Narwal, M. / Shin, Y. / Murakami, K.S.
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
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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