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- PDB-8yeh: HPV16 L1 pentamer in complex with Fab F5-196 -

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Basic information

Entry
Database: PDB / ID: 8yeh
TitleHPV16 L1 pentamer in complex with Fab F5-196
Components
  • Major capsid protein L1
  • heavy chain of F5-196
  • light chain of F5-196
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HPV16 / L1 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus type 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsWang, X. / Fu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HPV16 L1 pentamer in complex with Fab F5-196
Authors: Wang, X. / Fu, W.
History
DepositionFeb 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain of F5-196
B: light chain of F5-196
F: Major capsid protein L1
C: heavy chain of F5-196
H: light chain of F5-196
L: Major capsid protein L1
D: heavy chain of F5-196
I: light chain of F5-196
M: Major capsid protein L1
E: heavy chain of F5-196
J: light chain of F5-196
N: Major capsid protein L1
G: heavy chain of F5-196
K: light chain of F5-196
O: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)378,43015
Polymers378,43015
Non-polymers00
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: Antibody
heavy chain of F5-196


Mass: 13345.870 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody
light chain of F5-196


Mass: 11692.977 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein
Major capsid protein L1


Mass: 50647.133 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161H2J5
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

Component
IDNameTypeEntity IDParent-IDSource
1HPV16 L1 pentamer in complex with Fab F5-196COMPLEXall0RECOMBINANT
2FabF5-196COMPLEX#1-#21RECOMBINANT
3HPV16 L1 pentamerCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Human papillomavirus 16333760
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Escherichia coli (E. coli)562
32Homo sapiens (human)9606
Buffer solutionpH: 7.4
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: DARK FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 498615 / Symmetry type: POINT

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