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

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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: 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, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 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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