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- EMDB-75669: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75669
TitleCryo-EM structure of the bacteriophage N4 virion RNA polymerase (open plug state)
Map dataFull EM map
Sample
  • Complex: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase
    • Protein or peptide: Virion DNA-directed RNA polymerase
KeywordsN4 phage viral RNA polymerase / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 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 21, 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_75669.png

Downloads & links

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Map

FileDownload / File: emd_75669.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 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: 0.102
Minimum - Maximum-0.2754007 - 0.5975636
Average (Standard dev.)0.001648687 (±0.024028452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_75669_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_75669_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the bacteriophage N4 virion RNA polymerase

EntireName: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase
Components
  • Complex: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase
    • Protein or peptide: Virion DNA-directed RNA polymerase

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Supramolecule #1: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase

SupramoleculeName: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase in an open plug state
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 380 KDa

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Macromolecule #1: Virion DNA-directed RNA polymerase

MacromoleculeName: Virion DNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 276.245375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GIDAVYPSLV GTADSKAEGI KNYFKLSFTL PEEQKSRTVG SEAPLKDVAQ ALSSRARYEL FTEKETANPA FNGEVIKRYK ELMEHGEGI ADILRSRLAK FLNTKDVGKR FAQGTEANRW VGGKLLNIVE QDGDTFKYNE QLLQTAVLAG LQWRLTATSN T AIKDAKDV ...String:
GIDAVYPSLV GTADSKAEGI KNYFKLSFTL PEEQKSRTVG SEAPLKDVAQ ALSSRARYEL FTEKETANPA FNGEVIKRYK ELMEHGEGI ADILRSRLAK FLNTKDVGKR FAQGTEANRW VGGKLLNIVE QDGDTFKYNE QLLQTAVLAG LQWRLTATSN T AIKDAKDV AAITGIDQAL LPEGLVEQFD TGMTLTEAVS SLAQKIESYW GLSRNPNAPL GYTKGIPTAM AAEILAAFVE ST DVVENIV DMSEIDPDNK KTIGLYTITE LDSFDPINSF PTAIEEAVLV NPTEKMFFGD DIPPVANTQL RNPAVRNTPE QKA ALKAEQ ATEFYVHTPM VQFYETLGKD RILELMGAGT LNKELLNDNH AKSLEGKNRS VEDSYNQLFS VIEQVRAQSE DIST VPIHY AYNMTRVGRM QMLGKYNPQS AKLVREAILP TKATLDLSNQ NNEDFSAFQL GLAQALDIKV HTMTREVMSD ELTKL LEGN LKPAIDMMVE FNTTGSLPEN AVDVLNTALG DRKSFVALMA LMEYSRYLVA EDKSAFVTPL YVEADGVTNG PINAMM LMT GGLFTPDWIR NIAKGGLFIG SPNKTMNEHR STADNNDLYQ ASTNALMESL GKLRSNYASN MPIQSQIDSL LSLMDLF LP DINLGENGAL ELKRGIAKNP LTITIYGSGA RGIAGKLVSS VTDAIYERMS DVLKARAKDP NISAAMAMFG KQAASEAH A EELLARFLKD METLTSTVPV KRKGVLELQS TGTGAKGKIN PKTYTIKGEQ LKALQENMLH FFVEPLRNGI TQTVGESLV YSTEQLQKAT QIQSVVLEDM FKQRVQEKLA EKAKDPTWKK GDFLTQKELN DIQASLNNLA PMIETGSQTF YIAGSENAEV ANQVLATNL DDRMRVPMSI YAPAQAGVAG IPFMTIGTGD GMMMQTLSTM KGAPKNTLKI FDGMNIGLND ITDASRKANE A VYTSWQGN PIKNVYESYA KFMKNVDFSK LSPEALEAIG KSALEYDQRE NATVDDIANA ASLIERNLRN IALGVDIRHK VL DKVNLSI DQMAAVGAPY QNNGKIDLSN MTPEQQADEL NKLFREELEA RKQKVAKARA EVKEETVSEK EPVNPDFGMV GRE HKASGV RILSATAIRN LAKISNLPST QAATLAEIQK SLAAKDYKII YGTPTQVAEY ARQKNVTELT SQEMEEAQAG NIYG WTNFD DKTIYLVSPS METLIHELVH ASTFEEVYSF YQGNEVSPTS KQAIENLEGL MEQFRSLDIS KDSPEMREAY ADAIA TIEG HLSNGFVDPA ISKAAALNEF MAWGLANRAL AAKQKRTSSL VQMVKDVYQA IKKLIWGRKQ APALGEDMFS NLLFNS AIL MRSQPTTQAV AKDGTLFHSK AYGNNERLSQ LNQTFDKLVT DYLRTDPVTE VERRGNVANA LMSATRLVRD VQSHGFN MT AQEQSVFQMV TAALATEAAI DPHAMARAQE LYTHVMKHLT VEHFMADPDS TNPADRYYAQ QKYDTISGAN LVEVDAKG R TSLLPTFLGL AMVNEELRSI IKEMPVPKAD KKLGNDIDTL LTNAGTQVME SLNRRMAGDQ KATNVQDSID ALSETIMAA ALKRESFYDA VATPTGNFID RANQYVTDSI ERLSETVIEK ADKVIANPSN IAAKGVAHLA KLTAAIASEK QGEIVAQGVM TAMNQGKVW QPFHDLVNDI VGRTKTNANV YDLIKLVKSQ ISQDRQQFRE HLPTVIAGKF SRKLTDTEWS AMHTGLGKTD L AVLRETMS MAEIRDLLSS SKKVKDEIST LEKEIQNQAG RNWNLVQKKS KQLAQYMIMG EVGNNLLRNA HAISRLLGER IT NGPVADV AAIDKLITLY SLELMNKSDR DLLSELAQSE VEGMEFSIAY MVGQRTEEMR KAKGDNRTLL NHFKGYIPVE NQQ GVNLII ADDKEFAKLN SQSFTRIGTY QGSTGFRTGS KGYYFSPVAA RAPYSQGILQ NVRNTAGGVD IGTGFTLGTM VAGR ITDKP TVERITKALA KGERGREPLM PIYNSKGQVV AYEQSVDPNM LKHLNQDNHF AKMVGVWRGR QVEEAKAQRF NDILI EQLH AMYEKDIKDS SANKSQYVNL LGKIDDPVLA DAINLMNIET RHKAEELFGK DELWVRRDML NDALGYRAAS IGDVWT GNS RWSPSTLDTV KKMFLGAFGN KAYHVVMNAE NTIQNLVKDA KTVIVVKSVV VPAVNFLANI YQMIGRGVPV KDIAVNI PR KTSEINQYIK SRLRQIDAEA ELRAAEGNPN LVRKLKTEIQ SITDSHRRMS IWPLIEAGEF SSIADAGISR DDLLVAEG K IHEYMEKLAN KLPEKVRNAG RYALIAKDTA LFQGIQKTVE YSDFIAKAII YDDLVKRKKK SSSEALGQVT EEFINYDRL PGRFRGYMES MGLMWFYNFK IRSIKVAMSM IRNNPVHSLI ATVVPAPTMF GNVGLPIQDN MLTMLAEGRL DYSLGFGQGL RAPTLNPWF NLTH

UniProtKB: Virion DNA-directed RNA polymerase

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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 Active R2/1 / Material: COPPER / 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
DetailsMonodisperse sample of the vRNAP full length protein with all the domains intact

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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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.71) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.71) / Number images used: 57669
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.71)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.71)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.71)
FSC plot (resolution estimation)

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