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- PDB-8uej: ssRNA phage PhiCb5 virion -

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Basic information

Entry
Database: PDB / ID: 8uej
TitlessRNA phage PhiCb5 virion
Components
  • Coat protein
  • Maturation protein
KeywordsVIRUS / ssRNA phage
Function / homology: / Phage phiCb5, coat protein / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / viral capsid / Maturation protein / Coat protein
Function and homology information
Biological speciesCaulobacter phage phiCb5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang, Y. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R01GM141659 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.
Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang /
Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
History
DepositionOct 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Coat protein
AB: Coat protein
AC: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BQ: Coat protein
BR: Coat protein
BS: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EQ: Coat protein
ER: Coat protein
ES: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GY: Coat protein
GZ: Coat protein
HC: Coat protein
HD: Coat protein
HE: Coat protein
HI: Coat protein
HJ: Coat protein
HK: Coat protein
HO: Coat protein
HP: Coat protein
HQ: Coat protein
HU: Coat protein
HV: Coat protein
HW: Coat protein
IA: Coat protein
IB: Coat protein
IC: Coat protein
IG: Coat protein
IH: Coat protein
II: Coat protein
IM: Coat protein
IN: Coat protein
IO: Coat protein
IS: Coat protein
IT: Coat protein
IU: Coat protein
IY: Coat protein
IZ: Coat protein
JA: Coat protein
JE: Coat protein
JF: Coat protein
JG: Coat protein
JK: Coat protein
JL: Coat protein
JM: Coat protein
JQ: Coat protein
JR: Coat protein
JS: Coat protein
JW: Coat protein
JX: Coat protein
JY: Coat protein
KC: Coat protein
KD: Coat protein
KE: Coat protein
KI: Coat protein
KJ: Coat protein
KK: Coat protein
KO: Coat protein
KP: Coat protein
KQ: Coat protein
KU: Coat protein
KV: Coat protein
KW: Coat protein
LA: Coat protein
LB: Coat protein
LC: Coat protein
LG: Coat protein
LH: Coat protein
LI: Coat protein
LM: Coat protein
LN: Coat protein
LO: Coat protein
LS: Coat protein
LT: Coat protein
LU: Coat protein
LY: Coat protein
LZ: Coat protein
MA: Coat protein
ME: Coat protein
MF: Coat protein
MG: Coat protein
MK: Coat protein
ML: Coat protein
MM: Coat protein
MQ: Coat protein
MR: Coat protein
MS: Coat protein
MW: Coat protein
MX: Coat protein
NA: Coat protein
NB: Coat protein
NC: Coat protein
NG: Coat protein
NH: Coat protein
NI: Coat protein
NM: Coat protein
NN: Coat protein
NO: Coat protein
M: Maturation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,453,002415
Polymers2,443,544179
Non-polymers9,458236
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Coat protein


Mass: 13498.981 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC2
#2: Protein Maturation protein


Mass: 40725.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caulobacter phage phiCb5 (virus) / References: UniProt: D7RIC1
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 236 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: A complex of phiCb5 maturation protein and phiCb5 shell
Type: COMPLEX
Details: A complex of phiCb5 maturation protein and phiCb5 shell
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 2.1 MDa / Experimental value: NO
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Buffer solutionpH: 7.5 / Details: 20mM tris, 2mM MgCl2, 3mM CaCl2
Buffer component
IDConc.NameFormulaBuffer-ID
12 mMMagnesium chlorideMgCl21
220 mMTrisC4H11NO31
33 mMCalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.17.1_3660: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272204 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004176126
ELECTRON MICROSCOPYf_angle_d0.679238762
ELECTRON MICROSCOPYf_dihedral_angle_d5.27124610
ELECTRON MICROSCOPYf_chiral_restr0.04826788
ELECTRON MICROSCOPYf_plane_restr0.00630592

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