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- PDB-8xpm: Mature virion portal of phage lambda with DNA -

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Basic information

Entry
Database: PDB / ID: 8xpm
TitleMature virion portal of phage lambda with DNA
Components
  • DNA (104-MER)
  • DNA (92-MER)
  • Head completion protein
  • Head-tail connector protein FII
  • Portal protein B
  • Tail tube protein
  • Tail tube terminator protein
KeywordsVIRAL PROTEIN/DNA / Bacteriophage / caudovirales / siphoviridae / portal vertex / portal / capsid / connector/neck / tail / delivery device / B-DNA / VIRAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / virion assembly / viral life cycle / virion component / 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 / Minor tail protein U-like / Head-to-tail joining protein W superfamily / GpU-like superfamily / gpW / 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 / Minor tail protein U-like / Head-to-tail joining protein W superfamily / GpU-like superfamily / gpW / Phage minor tail protein U / Phage tail protein-like superfamily / Phage portal protein, lambda family / Phage portal protein, lambda family / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Portal protein B / Head-tail connector protein FII / Tail tube terminator protein / Tail tube protein / Head completion protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 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 4, 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
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Portal protein B
O: Tail tube protein
P: Tail tube protein
Q: Tail tube protein
R: Tail tube protein
U: Tail tube terminator protein
V: Tail tube protein
W: Head completion protein
DA: DNA (104-MER)
DB: DNA (92-MER)
f: Head-tail connector protein FII
w: Head completion protein
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
v: Tail tube protein
V1: Tail tube protein
v1: Tail tube protein
V2: Tail tube protein
v2: Tail tube protein
o: Tail tube protein
O1: Tail tube protein
o1: Tail tube protein
O2: Tail tube protein
o2: Tail tube protein
p: Tail tube protein
P1: Tail tube protein
p1: Tail tube protein
P2: Tail tube protein
p2: Tail tube protein
q: Tail tube protein
Q1: Tail tube protein
q1: Tail tube protein
Q2: Tail tube protein
q2: Tail tube protein
r: Tail tube protein
R1: Tail tube protein
r1: Tail tube protein
R2: Tail tube protein
r2: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)1,805,84668
Polymers1,805,84668
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 , 5 types, 66 molecules BbB1b1B2b2B3b3B4b4B5b5OPQRVvV1v1V2v2oO1o1O2o2pP1p1...

#1: 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
#2: Protein ...
Tail tube protein / TTP / Gene product V / gpV / Major tail protein V


Mass: 25831.779 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus) / References: UniProt: P03733
#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
Head completion protein / HCP / Head-tail joining protein W / 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
#7: Protein
Head-tail connector protein FII / Head-tail joining protein / 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

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DNA chain , 2 types, 2 molecules DADB

#5: DNA chain DNA (104-MER)


Mass: 32011.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus)
#6: DNA chain DNA (92-MER)


Mass: 28412.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Lambda (virus)

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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 Lambda / Type: VIRUS / Entity ID: #7, #4, #3, #1-#2, #5-#6 / 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19060 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 233.77 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0119122960
ELECTRON MICROSCOPYf_angle_d0.8284167833
ELECTRON MICROSCOPYf_chiral_restr0.045618700
ELECTRON MICROSCOPYf_plane_restr0.005721226
ELECTRON MICROSCOPYf_dihedral_angle_d13.250418430

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