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- PDB-8xck: Closed state of central tail fiber of bacteriophage lambda -

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Basic information

Entry
Database: PDB / ID: 8xck
TitleClosed state of central tail fiber of bacteriophage lambda
Components
  • Peptidyl-prolyl cis-trans isomerase A
  • Tip attachment protein J
KeywordsVIRUS / Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell ...symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / periplasmic space / virion attachment to host cell
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tip attachment protein J / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsGe, X.F. / Wang, J.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: To Be Published
Title: Cryo-EM structure of lambda tail with LamB
Authors: Ge, X.F. / Wang, J.W.
History
DepositionDec 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Tip attachment protein J
j: Peptidyl-prolyl cis-trans isomerase A
z: Peptidyl-prolyl cis-trans isomerase A
Z: Tip attachment protein J
f: Peptidyl-prolyl cis-trans isomerase A
F: Tip attachment protein J


Theoretical massNumber of molelcules
Total (without water)199,4976
Polymers199,4976
Non-polymers00
Water0
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 Tip attachment protein J


Mass: 46045.844 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03749
#2: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Rotamase A


Mass: 20453.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ppiA, rot, rotA, b3363, JW3326 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFL3, peptidylprolyl isomerase

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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

Component
IDNameTypeEntity IDParent-IDSource
1Bacteriophage lambda tail with LamBCOMPLEXall0RECOMBINANT
2tip attachment protein JCOMPLEX#11RECOMBINANT
3PPIACOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia phage Lambda (virus)2681611
33Escherichia coli (E. coli)562
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 369942 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410866
ELECTRON MICROSCOPYf_angle_d0.68714745
ELECTRON MICROSCOPYf_dihedral_angle_d6.4351473
ELECTRON MICROSCOPYf_chiral_restr0.0471695
ELECTRON MICROSCOPYf_plane_restr0.0071932

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