[English] 日本語
Yorodumi
- EMDB-71769: N4 vRNAP gp50 - Closed Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71769
TitleN4 vRNAP gp50 - Closed Complex
Map data
Sample
  • Complex: Full Length N4 Virion-Associated RNA Polymerase - Closed Complex
    • Protein or peptide: Virion DNA-directed RNA polymerase
KeywordsSingle Subunit RNA Polymerase / Bacteriophage Ejection Protein / VIRAL PROTEIN / TRANSFERASE
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: 2.8 Å
AuthorsBellis NF / Lokareddy RK / Cingolani G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
National Institutes of Health/Office of the DirectorOD024978 United States
CitationJournal: Res Sq / Year: 2025
Title: Structure of the giant RNA polymerase ejected from coliphage N4.
Authors: Nathan F Bellis / Ravi K Lokareddy / Mikhail Pavlenok / Stephanie L Cooper Horton / James L Kizziah / Francesca Forti / David A Schneider / Michael Niederweis / Federica Briani / Gino Cingolani /
Abstract: are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two ... are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two additional ejection proteins, to assemble a transient DNA-ejectosome that becomes transcriptionally active, initiating viral replication. Here, we present an integrative structural analysis of the coliphage N4 vRNAP (gp50). We find that this 383 kDa enzyme is a multi-domain, single-chain RNA polymerase, structurally distinct from both compact single-chain RNAPs and large multi-subunit holoenzymes. vRNAP is composed of loosely connected domains and exhibits an intramolecular mode of allosteric regulation through its C-terminal domain. Comparative analysis of intact and genome-released virions identified gp51, which forms an outer-membrane complex, and gp52, which assembles a periplasmic tunnel. These proteins generate heterogeneous pores that facilitate the release of vRNAP. We further uncover a signaling hub in the phage tail, composed of the receptor-binding protein, tail tube, and tail plug, that detects receptor engagement and orchestrates the release of ejection proteins. We propose that the beads-on-a-string architecture of vRNAP enables the translocation of megadalton-scale protein complexes through the ~35 Å channel formed by the tail and ejection proteins. These findings establish N4 as a distinctive model for protein translocation through biological channels.
History
DepositionJul 21, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71769.png

Downloads & links

-
Map

FileDownload / File: emd_71769.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 320 pix.
= 389.44 Å		1.22 Å/pix.
x 320 pix.
= 389.44 Å		1.22 Å/pix.
x 320 pix.
= 389.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.217 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0646
Minimum - Maximum-0.19447596 - 0.437205
Average (Standard dev.)0.002877633 (±0.010771257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 389.44 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_71769_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71769_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Full Length N4 Virion-Associated RNA Polymerase - Closed Complex

EntireName: Full Length N4 Virion-Associated RNA Polymerase - Closed Complex
Components
  • Complex: Full Length N4 Virion-Associated RNA Polymerase - Closed Complex
    • Protein or peptide: Virion DNA-directed RNA polymerase

-
Supramolecule #1: Full Length N4 Virion-Associated RNA Polymerase - Closed Complex

SupramoleculeName: Full Length N4 Virion-Associated RNA Polymerase - Closed Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage N4 (virus)

-
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: 382.9035 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 KTVIVVKAVV 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 221813
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4ff3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9pnr:
N4 vRNAP gp50 - Closed Complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more