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- PDB-8xqb: Mature virion portal vertex of bacteriophage lambda -

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Basic information

Entry
Database: PDB / ID: 8xqb
TitleMature virion portal vertex of bacteriophage lambda
Components
  • Capsid decoration protein
  • Head completion protein
  • Head-tail connector protein FII
  • Major capsid protein
  • Portal protein B
  • Tail tube terminator protein
KeywordsVIRAL PROTEIN / caudovirales / siphoviridae / portal / capsid / connector/neck / tail / delivery device / B-DNA / phage lambda
Function / homology
Function and homology information


viral capsid, decoration / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral tail assembly / viral DNA genome packaging / virus tail / T=7 icosahedral viral capsid / virion assembly / viral life cycle / virion component ...viral capsid, decoration / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral tail assembly / viral DNA genome packaging / virus tail / T=7 icosahedral viral capsid / virion assembly / viral life cycle / virion component / viral capsid / host cell cytoplasm / structural molecule activity / DNA binding
Similarity search - Function
Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / Head-to-tail joining protein W / Head-to-tail joining protein W superfamily / gpW / Minor tail protein U-like / Head decoration protein D superfamily / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily ...Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / Head-to-tail joining protein W / Head-to-tail joining protein W superfamily / gpW / Minor tail protein U-like / Head decoration protein D superfamily / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Head decoration protein D / Bacteriophage lambda head decoration protein D / Phage portal protein, lambda family / Phage portal protein, lambda family / Major capsid protein GpE / Phage major capsid protein E
Similarity search - Domain/homology
Portal protein B / Capsid decoration protein / Major capsid protein / Head-tail connector protein FII / Tail tube terminator protein / Head completion protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsWang, J.W. / Gu, Z.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: J Virol / Year: 2024
Title: Structural morphing in the viral portal vertex of bacteriophage lambda.
Authors: Zhiwei Gu / Kexun Wu / Jiawei Wang /
Abstract: The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA ...The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system.
IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple ...IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.
History
DepositionJan 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
f: Head-tail connector protein FII
W: Head completion protein
w: Head completion protein
U: Tail tube terminator protein
B: Portal protein B
b: Portal protein B
f1: Head-tail connector protein FII
W1: Head completion protein
w1: Head completion protein
U1: Tail tube terminator protein
B1: Portal protein B
b1: Portal protein B
f2: Head-tail connector protein FII
W2: Head completion protein
w2: Head completion protein
U2: Tail tube terminator protein
B2: Portal protein B
b2: Portal protein B
f3: Head-tail connector protein FII
W3: Head completion protein
w3: Head completion protein
U3: Tail tube terminator protein
B3: Portal protein B
b3: Portal protein B
f4: Head-tail connector protein FII
W4: Head completion protein
w4: Head completion protein
U4: Tail tube terminator protein
B4: Portal protein B
b4: Portal protein B
f5: Head-tail connector protein FII
W5: Head completion protein
w5: Head completion protein
U5: Tail tube terminator protein
B5: Portal protein B
b5: Portal protein B
A0: Major capsid protein
G0: Major capsid protein
C0: Major capsid protein
H0: Capsid decoration protein
I0: Capsid decoration protein
J0: Capsid decoration protein
N0: Capsid decoration protein
A1: Major capsid protein
G1: Major capsid protein
C1: Major capsid protein
H1: Capsid decoration protein
I1: Capsid decoration protein
J1: Capsid decoration protein
N1: Capsid decoration protein
A2: Major capsid protein
G2: Major capsid protein
C2: Major capsid protein
H2: Capsid decoration protein
I2: Capsid decoration protein
J2: Capsid decoration protein
N2: Capsid decoration protein
A3: Major capsid protein
G3: Major capsid protein
C3: Major capsid protein
H3: Capsid decoration protein
I3: Capsid decoration protein
J3: Capsid decoration protein
N3: Capsid decoration protein
A4: Major capsid protein
G4: Major capsid protein
C4: Major capsid protein
H4: Capsid decoration protein
I4: Capsid decoration protein
J4: Capsid decoration protein
N4: Capsid decoration protein


Theoretical massNumber of molelcules
Total (without water)1,775,56471
Polymers1,775,56471
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, 71 molecules ff1f2f3f4f5WwW1w1W2w2W3w3W4w4W5w5UU1U2U3U4U5BbB1b1B2b2...

#1: Protein
Head-tail connector protein FII / Minor capsid protein FII


Mass: 12775.037 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03714
#2: Protein
Head completion protein / gpW


Mass: 7625.749 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P68660
#3: Protein
Tail tube terminator protein / Gene product U / gpU


Mass: 14659.124 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03732
#4: Protein
Portal protein B / GpB / Minor capsid protein B


Mass: 59529.609 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03710
#5: Protein
Major capsid protein / Gene product E / gpE


Mass: 38229.160 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03713
#6: Protein
Capsid decoration protein / Gene product D / gpD / Major capsid protein D


Mass: 11582.873 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03712

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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 Lambda / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage Lambda (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SEROCOMPLEX / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9851 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 206.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029120983
ELECTRON MICROSCOPYf_angle_d0.5702163895
ELECTRON MICROSCOPYf_chiral_restr0.0417781
ELECTRON MICROSCOPYf_plane_restr0.004721595
ELECTRON MICROSCOPYf_dihedral_angle_d13.1344433

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