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- EMDB-75681: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (... -

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Basic information

Entry
Database: EMDB / ID: EMD-75681
TitleCryo-EM structure of the bacteriophage N4 virion RNA polymerase (closed plug state)
Map dataFull map
Sample
  • Complex: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (closed plug state)
    • Protein or peptide: Virion DNA-directed RNA polymerase
KeywordsBacteriophage N4 phage vRNAP protein / 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: 3.43 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_75681.png

Downloads & links

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Map

FileDownload / File: emd_75681.map.gz / Format: CCP4 / Size: 52.7 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 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-0.24639311 - 0.5657524
Average (Standard dev.)0.0017087456 (±0.023214469)
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 A

Fileemd_75681_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_75681_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 : Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (...

EntireName: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (closed plug state)
Components
  • Complex: Cryo-EM structure of the bacteriophage N4 virion RNA polymerase (closed plug state)
    • 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 (closed plug state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 274.2 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: 382.9195 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSVFDRLAGF ADSVTNAKQV DVSTATAQKK AEQGVTTPLV SPDAAYQMQA ARTGNVGANA FEPGTVQSDF MNLTPMQIMN KYGVEQGLQ LINARADAGN QVFNDSVTTR TPGEELGDIA TGVGLGFVNT LGGIGALGAG LLNDDAGAVV AQQLSKFNDA V HATQSQAL ...String:
MSVFDRLAGF ADSVTNAKQV DVSTATAQKK AEQGVTTPLV SPDAAYQMQA ARTGNVGANA FEPGTVQSDF MNLTPMQIMN KYGVEQGLQ LINARADAGN QVFNDSVTTR TPGEELGDIA TGVGLGFVNT LGGIGALGAG LLNDDAGAVV AQQLSKFNDA V HATQSQAL QDKRKLFAAR NLMNEVESER QYQTDKKEGT NDIVASLSKF GRDFVGSIEN AAQTDSIISD GLAEGVGSLL GA GPVLRGA SLLGKAVVPA NTLRSAALAG AIDAGTGTQS LARIASTVGR AAPGMVGVGA MEAGGAYQQT ADEIMKMSLK DLE KSPVYQ QHIKDGMSPE QARRQTASET GLTAAAIQLP IAAATGPLVS RFEMAPFRAG SLGAVGMNLA RETVEEGVQG ATGQ LAQNI AQQQNIDKNQ DLLKGVGTQA GLGALYGFGS AGVVQAPAGA ARLAGAATAP VLRTTMAGVK AAGSVAGKVV SPIKN TLVA RGERVMKQNE EASPVADDYV AQAAQEAMAQ APEAEVTIRD AVEATDATPE QKVAAHQYVS DLMNATRFNP ENYQEA PEH IRNAVAGSTD QVQVIQKLAD LVNTLDESNP QALMEAASYM YDAVSEFEQF INRDPAALDS IPKDSPAIEL LNRYTNL TA NIQNTPKVIG ALNVINRMIN ESAQNGSLNV TEESSPQEMQ NVALAAEVAP EKLNPESVNV VLKHAADGRI KLNNRQIA A LQNAAAILKG AREYDAEAAR LGLRPQDIVS KQIKTDESRT QEGQYSALQH ANRIRSAYNS GNFELASAYL NDFMQFAQH MQNKVGALNE HLVTGNADKN KSVHYQALTA DREWVRSRTG LGVNPYDTKS VKFAQQVALE AKTVADIANA LASAYPELKV SHIKVTPLD SRLNAPAAEV VKAFRQGNRD VASSQPKADS VNQVKETPVT KQEPVTSTVQ TKTPVSESVK TEPTTKESSP Q AIKEPVNQ SEKQDVNLTN EDNIKQPTES VKETETSTKE STVTEELKEG IDAVYPSLVG TADSKAEGIK NYFKLSFTLP EE QKSRTVG SEAPLKDVAQ ALSSRARYEL FTEKETANPA FNGEVIKRYK ELMEHGEGIA DILRSRLAKF LNTKDVGKRF AQG TEANRW VGGKLLNIVE QDGDTFKYNE QLLQTAVLAG LQWRLTATSN TAIKDAKDVA AITGIDQALL PEGLVEQFDT GMTL TEAVS SLAQKIESYW GLSRNPNAPL GYTKGIPTAM AAEILAAFVE STDVVENIVD MSEIDPDNKK TIGLYTITEL DSFDP INSF PTAIEEAVLV NPTEKMFFGD DIPPVANTQL RNPAVRNTPE QKAALKAEQA TEFYVHTPMV QFYETLGKDR ILELMG AGT LNKELLNDNH AKSLEGKNRS VEDSYNQLFS VIEQVRAQSE DISTVPIHYA YNMTRVGRMQ MLGKYNPQSA KLVREAI LP TKATLDLSNQ NNEDFSAFQL GLAQALDIKV HTMTREVMSD ELTKLLEGNL KPAIDMMVEF NTTGSLPENA VDVLNTAL G DRKSFVALMA LMEYSRYLVA EDKSAFVTPL YVEADGVTNG PINAMMLMTG GLFTPDWIRN IAKGGLFIGS PNKTMNEHR STADNNDLYQ ASTNALMESL GKLRSNYASN MPIQSQIDSL LSLMDLFLPD INLGENGALE LKRGIAKNPL TITIYGSGAR GIAGKLVSS VTDAIYERMS DVLKARAKDP NISAAMAMFG KQAASEAHAE ELLARFLKDM ETLTSTVPVK RKGVLELQST G TGAKGKIN PKTYTIKGEQ LKALQENMLH FFVEPLRNGI TQTVGESLVY STEQLQKATQ IQSVVLEDMF KQRVQEKLAE KA KDPTWKK GDFLTQKELN DIQASLNNLA PMIETGSQTF YIAGSENAEV ANQVLATNLD DRMRVPMSIY APAQAGVAGI PFM TIGTGD GMMMQTLSTM KGAPKNTLKI FDGMNIGLND ITDASRKANE AVYTSWQGNP IKNVYESYAK FMKNVDFSKL SPEA LEAIG KSALEYDQRE NATVDDIANA ASLIERNLRN IALGVDIRHK VLDKVNLSID QMAAVGAPYQ NNGKIDLSNM TPEQQ ADEL NKLFREELEA RKQKVAKARA EVKEETVSEK EPVNPDFGMV GREHKASGVR ILSATAIRNL AKISNLPSTQ AATLAE IQK SLAAKDYKII YGTPTQVAEY ARQKNVTELT SQEMEEAQAG NIYGWTNFDD KTIYLVSPSM ETLIHELVHA STFEEVY SF YQGNEVSPTS KQAIENLEGL MEQFRSLDIS KDSPEMREAY ADAIATIEGH LSNGFVDPAI SKAAALNEFM AWGLANRA L AAKQKRTSSL VQMVKDVYQA IKKLIWGRKQ APALGEDMFS NLLFNSAILM RSQPTTQAVA KDGTLFHSKA YGNNERLSQ LNQTFDKLVT DYLRTDPVTE VERRGNVANA LMSATRLVRD VQSHGFNMTA QEQSVFQMVT AALATEAAID PHAMARAQEL YTHVMKHLT VEHFMADPDS TNPADRYYAQ QKYDTISGAN LVEVDAKGRT SLLPTFLGLA MVNEELRSII KEMPVPKADK K LGNDIDTL LTNAGTQVME SLNRRMAGDQ KATNVQDSID ALSETIMAAA LKRESFYDAV ATPTGNFIDR ANQYVTDSIE RL SETVIEK ADKVIANPSN IAAKGVAHLA KLTAAIASEK QGEIVAQGVM TAMNQGKVWQ PFHDLVNDIV GRTKTNANVY DLI KLVKSQ ISQDRQQFRE HLPTVIAGKF SRKLTDTEWS AMHTGLGKTD LAVLRETMSM AEIRDLLSSS KKVKDEISTL EKEI QNQAG RNWNLVQKKS KQLAQYMIMG EVGNNLLRNA HAISRLLGER ITNGPVADVA AIDKLITLYS LELMNKSDRD LLSEL AQSE VEGMEFSIAY MVGQRTEEMR KAKGDNRTLL NHFKGYIPVE NQQGVNLIIA DDKEFAKLNS QSFTRIGTYQ GSTGFR TGS KGYYFSPVAA RAPYSQGILQ NVRNTAGGVD IGTGFTLGTM VAGRITDKPT VERITKALAK GERGREPLMP IYNSKGQ VV AYEQSVDPNM LKHLNQDNHF AKMVGVWRGR QVEEAKAQRF NDILIEQLHA MYEKDIKDSS ANKSQYVNLL GKIDDPVL A DAINLMNIET RHKAEELFGK DELWVRRDML NDALGYRAAS IGDVWTGNSR WSPSTLDTVK KMFLGAFGNK AYHVVMNAE NTIQNLVKDA KTVIVVKSVV VPAVNFLANI YQMIGRGVPV KDIAVNIPRK TSEINQYIKS RLRQIDAEAE LRAAEGNPNL VRKLKTEIQ SITDSHRRMS IWPLIEAGEF SSIADAGISR DDLLVAEGKI HEYMEKLANK LPEKVRNAGR YALIAKDTAL F QGIQKTVE YSDFIAKAII YDDLVKRKKK SSSEALGQVT EEFINYDRLP GRFRGYMESM GLMWFYNFKI RSIKVAMSMI RN NPVHSLI ATVVPAPTMF GNVGLPIQDN MLTMLAEGRL DYSLGFGQGL RAPTLNPWFN LTH

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 R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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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 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 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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