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- EMDB-75680: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75680
TitleCryo-EM structure of the bacteriophage N4 virion RNA polymerase (transcription initiation complex)
Map dataFull map
Sample
  • Complex: minivRNAP with the hairpin promoter in a transcribing state
    • Protein or peptide: Virion DNA-directed RNA polymerase
    • DNA: 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')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsN4 Bacteriophage vRNAP / VIRAL PROTEIN
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
Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesEscherichia phage N4 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsNarwal M / Shin Y / Murakami KS
Funding support1 items
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 KS
History
DepositionFeb 23, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75680.png

Downloads & links

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Map

FileDownload / File: emd_75680.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242
Minimum - Maximum-0.08742817 - 0.23783414
Average (Standard dev.)0.0003452535 (±0.009209461)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_75680_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_75680_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : minivRNAP with the hairpin promoter in a transcribing state

EntireName: minivRNAP with the hairpin promoter in a transcribing state
Components
  • Complex: minivRNAP with the hairpin promoter in a transcribing state
    • Protein or peptide: Virion DNA-directed RNA polymerase
    • DNA: 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')
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: minivRNAP with the hairpin promoter in a transcribing state

SupramoleculeName: minivRNAP with the hairpin promoter in a transcribing state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 119.9 KDa

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Macromolecule #1: Virion DNA-directed RNA polymerase

MacromoleculeName: Virion DNA-directed RNA polymerase / type: protein_or_peptide / ID: 1
Details: ...Details: MSVFDRLAGFADSVTNAKQVDVSTATAQKKAEQGVTTPLVSPDAAYQMQAARTGNVGANAFEPGTVQSDFMNLTPMQIMNKYGVEQGLQLINARADAGNQVFNDSVTTRTPGEELGDIATGVGLGFVNTLGGIGALGAGLLNDDAGAVVAQQLSKFNDAVHATQSQALQDKRKLFAARNLMNEVESERQYQTDKKEGTNDIVASLSKFGRDFVGSIENAAQTDSIISDGLAEGVGSLLGAGPVLRGASLLGKAVVPANTLRSAALAGAIDAGTGTQSLARIASTVGRAAPGMVGVGAMEAGGAYQQTADEIMKMSLKDLEKSPVYQQHIKDGMSPEQARRQTASETGLTAAAIQLPIAAATGPLVSRFEMAPFRAGSLGAVGMNLARETVEEGVQGATGQLAQNIAQQQNIDKNQDLLKGVGTQAGLGALYGFGSAGVVQAPAGAARLAGAATAPVLRTTMAGVKAAGSVAGKVVSPIKNTLVARGERVMKQNEEASPVADDYVAQAAQEAMAQAPEAEVTIRDAVEATDATPEQKVAAHQYVSDLMNATRFNPENYQEAPEHIRNAVAGSTDQVQVIQKLADLVNTLDESNPQALMEAASYMYDAVSEFEQFINRDPAALDSIPKDSPAIELLNRYTNLTANIQNTPKVIGALNVINRMINESAQNGSLNVTEESSPQEMQNVALAAEVAPEKLNPESVNVVLKHAADGRIKLNNRQIAALQNAAAILKGAREYDAEAARLGLRPQDIVSKQIKTDESRTQEGQYSALQHANRIRSAYNSGNFELASAYLNDFMQFAQHMQNKVGALNEHLVTGNADKNKSVHYQALTADREWVRSRTGLGVNPYDTKSVKFAQQVALEAKTVADIANALASAYPELKVSHIKVTPLDSRLNAPAAEVVKAFRQGNRDVASSQPKADSVNQVKETPVTKQEPVTSTVQTKTPVSESVKTEPTTKESSPQAIKEPVNQSEKQDVNLTNEDNIKQPTESVKETETSTKESTVTEELKEGIDAVYPSLVGTADSKAEGIKNYFKLSFTLPEEQKSRTVGSEAPLKDVAQALSSRARYELFTEKETANPAFNGEVIKRYKELMEHGEGIADILRSRLAKFLNTKDVGKRFAQGTEANRWVGGKLLNIVEQDGDTFKYNEQLLQTAVLAGLQWRLTATSNTAIKDAKDVAAITGIDQALLPEGLVEQFDTGMTLTEAVSSLAQKIESYWGLSRNPNAPLGYTKGIPTAMAAEILAAFVESTDVVENIVDMSEIDPDNKKTIGLYTITELDSFDPINSFPTAIEEAVLVNPTEKMFFGDDIPPVANTQLRNPAVRNTPEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAGTLNKELLNDNHAKSLEGKNRSVEDSYNQLFSVIEQVRAQSEDISTVPIHYAYNMTRVGRMQMLGKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLGLAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAEDKSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKLRSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVSSVTDAIYERMSDVLKARAKDPNISAAMAMFGKQAASEAHAEELLARFLKDMETLTSTVPVKRKGVLELQSTGTGAKGKINPKTYTIKGEQLKALQENMLHFFVEPLRNGITQTVGESLVYSTEQLQKATQIQSVVLEDMFKQRVQEKLAEKAKDPTWKKGDFLTQKELNDIQASLNNLAPMIETGSQTFYIAGSENAEVANQVLATNLDDRMRVPMSIYAPAQAGVAGIPFMTIGTGDGMMMQTLSTMKGAPKNTLKIFDGMNIGLNDITDASRKANEAVYTSWQGNPIKNVYESYAKFMKNVDFSKLSPEALEAIGKSALEYDQRENATVDDIANAASLIERNLRNIALGVDIRHKVLDKVNLSIDQMAAVGAPYQNNGKIDLSNMTPEQQADELNKLFREELEARKQKVAKARAEVKEETVSEKEPVNPDFGMVGREHKASGVRILSATAIRNLAKISNLPSTQAATLAEIQKSLAAKDYKIIYGTPTQVAEYARQKNVTELTSQEMEEAQAGNIYGWTNFDDKTIYLVSPSMETLIHELVHASTFEEVYSFYQGNEVSPTSKQAIENLEGLMEQFRSLDISKDSPEMREAYADAIATIEGHLSNGFVDPAISKAAALNEFMAWGLANRALAAKQKRTSSLVQMVKDVYQAIKKLIWGRKQAPALGEDMFSNLLFNSAILMRSQPTTQAVAKDGTLFHSKAYGNNERLSQLNQTFDKLVTDYLRTDPVTEVERRGNVANALMSATRLVRDVQSHGFNMTAQEQSVFQMVTAALATEAAIDPHAMARAQELYTHVMKHLTVEHFMADPDSTNPADRYYAQQKYDTISGANLVEVDAKGRTSLLPTFLGLAMVNEELRSIIKEMPVPKADKKLGNDIDTLLTNAGTQVMESLNRRMAGDQKATNVQDSIDALSETIMAAALKRESFYDAVATPTGNFIDRANQYVTDSIERLSETVIEKADKVIANPSNIAAKGVAHLAKLTAAIASEKQGEIVAQGVMTAMNQGKVWQPFHDLVNDIVGRTKTNANVYDLIKLVKSQISQDRQQFREHLPTVIAGKFSRKLTDTEWSAMHTGLGKTDLAVLRETMSMAEIRDLLSSSKKVKDEISTLEKEIQNQAGRNWNLVQKKSKQLAQYMIMGEVGNNLLRNAHAISRLLGERITNGPVADVAAIDKLITLYSLELMNKSDRDLLSELAQSEVEGMEFSIAYMVGQRTEEMRKAKGDNRTLLNHFKGYIPVENQQGVNLIIADDKEFAKLNSQSFTRIGTYQGSTGFRTGSKGYYFSPVAARAPYSQGILQNVRNTAGGVDIGTGFTLGTMVAGRITDKPTVERITKALAKGERGREPLMPIYNSKGQVVAYEQSVDPNMLKHLNQDNHFAKMVGVWRGRQVEEAKAQRFNDILIEQLHAMYEKDIKDSSANKSQYVNLLGKIDDPVLADAINLMNIETRHKAEELFGKDELWVRRDMLNDALGYRAASIGDVWTGNSRWSPSTLDTVKKMFLGAFGNKAYHVVMNAENTIQNLVKDAKTVIVVKSVVVPAVNFLANIYQMIGRGVPVKDIAVNIPRKTSEINQYIKSRLRQIDAEAELRAAEGNPNLVRKLKTEIQSITDSHRRMSIWPLIEAGEFSSIADAGISRDDLLVAEGKIHEYMEKLANKLPEKVRNAGRYALIAKDTALFQGIQKTVEYSDFIAKAIIYDDLVKRKKKSSSEALGQVTEEFINYDRLPGRFRGYMESMGLMWFYNFKIRSIKVAMSMIRNNPVHSLIATVVPAPTMFGNVGLPIQDNMLTMLAEGRLDYSLGFGQGLRAPTLNPWFNLTH
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 359.89125 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: SVFDRLAGFA DSVTNAKQVD VSTATAQKKA EQGVTTPLVS PDAAYQMQAA RTGNVGANAF EPGTVQSDFM NLTPMQIMNK YGVEQGLQL INARADAGNQ VFNDSVTTRT PGEELGDIAT GVGLGFVNTL GGIGALGAGL LNDDAGAVVA QQLSKFNDAV H ATQSQALQ ...String:
SVFDRLAGFA DSVTNAKQVD VSTATAQKKA EQGVTTPLVS PDAAYQMQAA RTGNVGANAF EPGTVQSDFM NLTPMQIMNK YGVEQGLQL INARADAGNQ VFNDSVTTRT PGEELGDIAT GVGLGFVNTL GGIGALGAGL LNDDAGAVVA QQLSKFNDAV H ATQSQALQ DKRKLFAARN LMNEVESERQ YQTDKKEGTN DIVASLSKFG RDFVGSIENA AQTDSIISDG LAEGVGSLLG AG PVLRGAS LLGKAVVPAN TLRSAALAGA IDAGTGTQSL ARIASTVGRA APGMVGVGAM EAGGAYQQTA DEIMKMSLKD LEK SPVYQQ HIKDGMSPEQ ARRQTASETG LTAAAIQLPI AAATGPLVSR FEMAPFRAGS LGAVGMNLAR ETVEEGVQGA TGQL AQNIA QQQNIDKNQD LLKGVGTQAG LGALYGFGSA GVVQAPAGAA RLAGAATAPV LRTTMAGVKA AGSVAGKVVS PIKNT LVAR GERVMKQNEE ASPVADDYVA QAAQEAMAQA PEAEVTIRDA VEATDATPEQ KVAAHQYVSD LMNATRFNPE NYQEAP EHI RNAVAGSTDQ VQVIQKLADL VNTLDESNPQ ALMEAASYMY DAVSEFEQFI NRDPAALDSI PKDSPAIELL NRYTNLT AN IQNTPKVIGA LNVINRMINE SAQNGSLNVT EESSPQEMQN VALAAEVAPE KLNPESVNVV LKHAADGRIK LNNRQIAA L QNAAAILKGA REYDAEAARL GLRPQDIVSK QIKTDESRTQ EGQYSALQHA NRIRSAYNSG NFELASAYLN DFMQFAQHM QNKVGALNEH LVTGNADKNK SVHYQALTAD REWVRSRTGL GVNPYDTKSV KFAQQVALEA KTVADIANAL ASAYPELKVS HIKVTPLDS RLNAPAAEVV KAFRQGNRDV ASSQPKADSV NQVKETPVTK QEPVTSTVQT KTPVSESVKT EPTTKESSPQ A IKEPVNQS EKQDVNLTNE DNIKQPTESV KETETSTKES TVTEELKEGI DAVYPSLVGT ADSKAEGIKN YFKLSFTLPE EQ KSRTVGS EAPLKDVAQA LSSRARYELF TEKETANPAF NGEVIKRYKE LMEHGEGIAD ILRSRLAKFL NTKDVGKRFA QGT EANRWV GGKLLNIVEQ DGDTFKYNEQ LLQTAVLAGL QWRLTATSNT AIKDAKDVAA ITGIDQALLP EGLVEQFDTG MTLT EAVSS LAQKIESYWG LSRNPNAPLG YTKGIPTAMA AEILAAFVES TDVVENIVDM SEIDPDNKKT IGLYTITELD SFDPI NSFP TAIEEAVLVN PTEKMFFGDD IPPVANTQLR NPAVRNTPEQ KAALKAEQAT EFYVHTPMVQ FYETLGKDRI LELMGA GTL NKELLNDNHA KSLEGKNRSV EDSYNQLFSV IEQVRAQSED ISTVPIHYAY NMTRVGRMQM LGKYNPQSAK LVREAIL PT KATLDLSNQN NEDFSAFQLG LAQALDIKVH TMTREVMSDE LTKLLEGNLK PAIDMMVEFN TTGSLPENAV DVLNTALG D RKSFVALMAL MEYSRYLVAE DKSAFVTPLY VEADGVTNGP INAMMLMTGG LFTPDWIRNI AKGGLFIGSP NKTMNEHRS TADNNDLYQA STNALMESLG KLRSNYASNM PIQSQIDSLL SLMDLFLPDI NLGENGALEL KRGIAKNPLT ITIYGSGARG IAGKLVSSV TDAIYERMSD VLKARAKDPN ISAAMAMFGK QAASEAHAEE LLARFLKDME TLTSTVPVKR KGVLELQSTG T GAKGKINP KTYTIKGEQL KALQENMLHF FVEPLRNGIT QTVGESLVYS TEQLQKATQI QSVVLEDMFK QRVQEKLAEK AK DPTWKKG DFLTQKELND IQASLNNLAP MIETGSQTFY IAGSENAEVA NQVLATNLDD RMRVPMSIYA PAQAGVAGIP FMT IGTGDG MMMQTLSTMK GAPKNTLKIF DGMNIGLNDI TDASRKANEA VYTSWQGNPI KNVYESYAKF MKNVDFSKLS PEAL EAIGK SALEYDQREN ATVDDIANAA SLIERNLRNI ALGVDIRHKV LDKVNLSIDQ MAAVGAPYQN NGKIDLSNMT PEQQA DELN KLFREELEAR KQKVAKARAE VKEETVSEKE PVNPDFGMVG REHKASGVRI LSATAIRNLA KISNLPSTQA ATLAEI QKS LAAKDYKIIY GTPTQVAEYA RQKNVTELTS QEMEEAQAGN IYGWTNFDDK TIYLVSPSME TLIHELVHAS TFEEVYS FY QGNEVSPTSK QAIENLEGLM EQFRSLDISK DSPEMREAYA DAIATIEGHL SNGFVDPAIS KAAALNEFMA WGLANRAL A AKQKRTSSLV QMVKDVYQAI KKLIWGRKQA PALGEDMFSN LLFNSAILMR SQPTTQAVAK DGTLFHSKAY GNNERLSQL NQTFDKLVTD YLRTDPVTEV ERRGNVANAL MSATRLVRDV QSHGFNMTAQ EQSVFQMVTA ALATEAAIDP HAMARAQELY THVMKHLTV EHFMADPDST NPADRYYAQQ KYDTISGANL VEVDAKGRTS LLPTFLGLAM VNEELRSIIK EMPVPKADKK L GNDIDTLL TNAGTQVMES LNRRMAGDQK ATNVQDSIDA LSETIMAAAL KRESFYDAVA TPTGNFIDRA NQYVTDSIER LS ETVIEKA DKVIANPSNI AAKGVAHLAK LTAAIASEKQ GEIVAQGVMT AMNQGKVWQP FHDLVNDIVG RTKTNANVYD LIK LVKSQI SQDRQQFREH LPTVIAGKFS RKLTDTEWSA MHTGLGKTDL AVLRETMSMA EIRDLLSSSK KVKDEISTLE KEIQ NQAGR NWNLVQKKSK QLAQYMIMGE VGNNLLRNAH AISRLLGERI TNGPVADVAA IDKLITLYSL ELMNKSDRDL LSELA QSEV EGMEFSIAYM VGQRTEEMRK AKGDNRTLLN HFKGYIPVEN QQGVNLIIAD DKEFAKLNSQ SFTRIGTYQG STGFRT GSK GYYFSPVAAR APYSQGILQN VRNTAGGVDI GTGFTLGTMV AGRITDKPTV ERITKALAKG ERGREPLMPI YNSKGQV VA YEQSVDPNML KHLNQDNHFA KMVGVWRGRQ VEEAKAQRFN DILIEQLHAM YEKDIKDSSA NKSQYVNLLG KIDDPVLA D AINLMNIETR HKAEELFGKD ELWVRRDMLN DALGYRAASI GDVWTGNSRW SPSTLDTVKK MFLGAFGNKA YHVVMNAEN TIQNLVKDAK TVIVVKSVVV PAVNFLANIY QMIGRGVPVK DIAVNIPRKT SEINQYIKSR LRQIDAEAEL RAAEGNPNLV RKLKTEIQS ITDSHRR

UniProtKB: Virion DNA-directed RNA polymerase

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Macromolecule #2: DNA (5'-D(P*AP*AP*CP*CP*AP*AP*AP*AP*GP*AP*AP*GP*CP*GP*GP*AP*GP*CP...

MacromoleculeName: 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')
type: dna / ID: 2 / Details: promoter consensus sequence / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.615819 KDa
SequenceString:
(DC)(DA)(DT)(DT)(DT)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DA)(DA)(DG)(DA)(DA)(DC)(DG)(DA) (DA)(DC)(DA)(DA)(DC)(DC)(DA)(DA)(DA) (DA)(DG)(DA)(DA)(DG)(DC)(DG)(DG)(DA)(DG) (DC) (DT)(DT)(DC)(DT)

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-11go:
Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (transcription initiation complex)

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