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- PDB-8tux: Capsid of mature PP7 virion with 3'end region of PP7 genomic RNA -

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Basic information

Entry
Database: PDB / ID: 8tux
TitleCapsid of mature PP7 virion with 3'end region of PP7 genomic RNA
Components
  • 3'end of PP7 genomic RNA
  • Capsid proteinCapsid
  • Maturation protein A
KeywordsVIRAL PROTEIN / Maturation protein / PP7 / pepevirus
Function / homology
Function and homology information


virion attachment to host cell pilus / T=3 icosahedral viral capsid / virion component / regulation of translation / symbiont entry into host cell / RNA binding / identical protein binding
Similarity search - Function
Bacteriophage PP7, coat / Phage PP7 coat protein / Assembly protein / Phage maturation protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Capsid protein / Maturation protein A
Similarity search - Component
Biological speciesPseudomonas phage PP7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsThongchol, J. / Zhang, J. / Zeng, L.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI156846 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141659 United States
National Science Foundation (NSF, United States)MCB-1902392 United States
Other privateTexas A and M University T3 United States
Other privateTexas A and M University X-grants United States
Other privateTexas A and M University, Center for phage technology grant United States
National Science Foundation (NSF, United States)PHY-1734030 United States
CitationJournal: Science / Year: 2024
Title: Removal of type IV pili by a small RNA virus.
Authors: Jirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng /
Abstract: The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: 3'end of PP7 genomic RNA
m: Maturation protein A
M: Maturation protein A
a1: Capsid protein
b1: Capsid protein
c1: Capsid protein
d1: Capsid protein
e1: Capsid protein
f1: Capsid protein
g1: Capsid protein
h1: Capsid protein
i1: Capsid protein
j1: Capsid protein
k1: Capsid protein
l1: Capsid protein
m1: Capsid protein
n1: Capsid protein
o1: Capsid protein
p1: Capsid protein
q1: Capsid protein
r1: Capsid protein
s1: Capsid protein
t1: Capsid protein
u1: Capsid protein
v1: Capsid protein
w1: Capsid protein
x1: Capsid protein
y1: Capsid protein
z1: Capsid protein
A1: Capsid protein
B1: Capsid protein
C1: Capsid protein
D1: Capsid protein
E1: Capsid protein
F1: Capsid protein
G1: Capsid protein
H1: Capsid protein
I1: Capsid protein
J1: Capsid protein
K1: Capsid protein
L1: Capsid protein
M1: Capsid protein
N1: Capsid protein
O1: Capsid protein
P1: Capsid protein
Q1: Capsid protein
R1: Capsid protein
S1: Capsid protein
T1: Capsid protein
U1: Capsid protein
V1: Capsid protein
W1: Capsid protein
X1: Capsid protein
Y1: Capsid protein
Z1: Capsid protein
01: Capsid protein
11: Capsid protein
21: Capsid protein
31: Capsid protein
41: Capsid protein
51: Capsid protein
61: Capsid protein
71: Capsid protein
A2: Capsid protein
B2: Capsid protein
C2: Capsid protein
D2: Capsid protein
E2: Capsid protein
F2: Capsid protein
G2: Capsid protein
H2: Capsid protein
I2: Capsid protein
J2: Capsid protein
K2: Capsid protein
L2: Capsid protein
M2: Capsid protein
N2: Capsid protein
O2: Capsid protein
P2: Capsid protein
Q2: Capsid protein
R2: Capsid protein
S2: Capsid protein
T2: Capsid protein
U2: Capsid protein
V2: Capsid protein
W2: Capsid protein
X2: Capsid protein
Y2: Capsid protein
Z2: Capsid protein
a2: Capsid protein
b2: Capsid protein
c2: Capsid protein
d2: Capsid protein
e2: Capsid protein
f2: Capsid protein
g2: Capsid protein
h2: Capsid protein
i2: Capsid protein
j2: Capsid protein
k2: Capsid protein
l2: Capsid protein
m2: Capsid protein
n2: Capsid protein
o2: Capsid protein
p2: Capsid protein
q2: Capsid protein
r2: Capsid protein
s2: Capsid protein
t2: Capsid protein
u2: Capsid protein
v2: Capsid protein
w2: Capsid protein
x2: Capsid protein
y2: Capsid protein
z2: Capsid protein
02: Capsid protein
12: Capsid protein
22: Capsid protein
32: Capsid protein
42: Capsid protein
52: Capsid protein
62: Capsid protein
72: Capsid protein
82: Capsid protein
92: Capsid protein
2a: Capsid protein
2b: Capsid protein
2c: Capsid protein
2d: Capsid protein
2e: Capsid protein
2f: Capsid protein
2g: Capsid protein
2h: Capsid protein
2i: Capsid protein
2j: Capsid protein
2k: Capsid protein
2l: Capsid protein
2m: Capsid protein
2n: Capsid protein
2o: Capsid protein
2p: Capsid protein
2q: Capsid protein
2r: Capsid protein
2s: Capsid protein
2t: Capsid protein
2u: Capsid protein
2v: Capsid protein
2w: Capsid protein
2x: Capsid protein
2y: Capsid protein
2z: Capsid protein
2A: Capsid protein
2B: Capsid protein
2C: Capsid protein
2D: Capsid protein
2E: Capsid protein
2F: Capsid protein
2G: Capsid protein
2H: Capsid protein
2I: Capsid protein
2J: Capsid protein
2K: Capsid protein
2L: Capsid protein
2M: Capsid protein
2N: Capsid protein
2O: Capsid protein
2P: Capsid protein
2Q: Capsid protein
2R: Capsid protein
2S: Capsid protein
2T: Capsid protein
2U: Capsid protein
2V: Capsid protein
2W: Capsid protein
2X: Capsid protein
2Y: Capsid protein
2Z: Capsid protein
aa: Capsid protein
ab: Capsid protein
ac: Capsid protein
ad: Capsid protein


Theoretical massNumber of molelcules
Total (without water)2,607,396181
Polymers2,607,396181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain 3'end of PP7 genomic RNA


Mass: 30456.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage PP7 (virus) / References: GenBank: NC_001628
#2: Protein Maturation protein A / MP / Assembly protein / A protein


Mass: 50763.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage PP7 (virus) / References: UniProt: Q38061
#3: Protein ...
Capsid protein / Capsid / CP / Coat protein


Mass: 13906.811 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage PP7 (virus) / References: UniProt: P03630

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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: Pseudomonas phage PP7 / Type: COMPLEX
Details: Maturation proteins of PP7, 3'end region of PP7 genomic RNA, coat protein shell of PP7
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas phage PP7 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
Virus shellDiameter: 280 nm
Buffer solutionpH: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4
Buffer componentConc.: 1 x / Name: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 51.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
4RELIONCTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 644601 / Symmetry type: POINT

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