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- PDB-9yf5: N4 Empty Particle C6 Tail -

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Basic information

Entry
Database: PDB / ID: 9yf5
TitleN4 Empty Particle C6 Tail
Components
  • 30 kDa protein
  • 60 kDa protein
  • Gp54
  • Gp64
  • Non-contractile tail sheath
  • Probable portal protein
KeywordsVIRAL PROTEIN / dodecamer / bacteriophage portal
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / adhesion receptor-mediated virion attachment to host cell / virion component / symbiont entry into host cell
Similarity search - Function
: / Non-contractile tail sheath N-terminal domain / Non-contractile tail sheath protein TIM barrel / : / SU10 adaptor protein / : / Phage SU10 portal protein / Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Probable portal protein / Gp64 / Non-contractile tail sheath / 60 kDa protein / 30 kDa protein / Gp54
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBellis, N.F. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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
DepositionSep 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: 30 kDa protein
AB: 30 kDa protein
LA: Non-contractile tail sheath
SA: Gp64
TA: Gp54
TB: Gp54
XA: 60 kDa protein
XB: 60 kDa protein
YA: 60 kDa protein
YB: 60 kDa protein
ZA: 60 kDa protein
ZB: 60 kDa protein
PA: Probable portal protein
AC: 30 kDa protein
AD: 30 kDa protein
LB: Non-contractile tail sheath
SB: Gp64
TC: Gp54
TD: Gp54
XC: 60 kDa protein
XD: 60 kDa protein
YC: 60 kDa protein
YD: 60 kDa protein
ZC: 60 kDa protein
ZD: 60 kDa protein
AE: 30 kDa protein
AF: 30 kDa protein
LC: Non-contractile tail sheath
SC: Gp64
TE: Gp54
TF: Gp54
XE: 60 kDa protein
XF: 60 kDa protein
YE: 60 kDa protein
YF: 60 kDa protein
ZE: 60 kDa protein
ZF: 60 kDa protein
AG: 30 kDa protein
AH: 30 kDa protein
LD: Non-contractile tail sheath
SD: Gp64
TG: Gp54
TH: Gp54
XG: 60 kDa protein
XH: 60 kDa protein
YG: 60 kDa protein
YH: 60 kDa protein
ZG: 60 kDa protein
ZH: 60 kDa protein
AI: 30 kDa protein
AJ: 30 kDa protein
LE: Non-contractile tail sheath
SE: Gp64
TI: Gp54
TJ: Gp54
XI: 60 kDa protein
XJ: 60 kDa protein
YI: 60 kDa protein
YJ: 60 kDa protein
ZI: 60 kDa protein
ZJ: 60 kDa protein
AK: 30 kDa protein
AL: 30 kDa protein
LF: Non-contractile tail sheath
SF: Gp64
TK: Gp54
TL: Gp54
XK: 60 kDa protein
XL: 60 kDa protein
YK: 60 kDa protein
YL: 60 kDa protein
ZK: 60 kDa protein
ZL: 60 kDa protein
PB: Probable portal protein
PC: Probable portal protein
PD: Probable portal protein
PE: Probable portal protein
PF: Probable portal protein
PG: Probable portal protein
PH: Probable portal protein
PI: Probable portal protein
PJ: Probable portal protein
PK: Probable portal protein
PL: Probable portal protein


Theoretical massNumber of molelcules
Total (without water)5,079,39684
Polymers5,079,39684
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 6 types, 84 molecules AAABACADAEAFAGAHAIAJAKALLALBLCLDLELFSASBSCSDSESFTATBTCTDTETF...

#1: Protein
30 kDa protein


Mass: 27192.412 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE9
#2: Protein
Non-contractile tail sheath / Gene product 65 / Gp65


Mass: 154255.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE7
#3: Protein
Gp64


Mass: 48100.742 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE6
#4: Protein
Gp54


Mass: 32438.443 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: Q859Q3
#5: Protein ...
60 kDa protein


Mass: 58943.914 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE8
#6: Protein
Probable portal protein / 94 kDa protein / Gene product 59 / gp59 / Head-to-tail connector


Mass: 85642.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE1

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia phage N4 / Type: VIRUS / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Escherichia coli str. K-12 substr. MG1655
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10265 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001211722
ELECTRON MICROSCOPYf_angle_d0.367287724
ELECTRON MICROSCOPYf_dihedral_angle_d8.6978378
ELECTRON MICROSCOPYf_chiral_restr0.03831848
ELECTRON MICROSCOPYf_plane_restr0.00337530

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