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- PDB-9ml1: D24.1M01 Fab bound to HPV16 L1 pentamer -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9ml1
TitleD24.1M01 Fab bound to HPV16 L1 pentamer
Components
  • D24.1M01 Heavy Chain
  • D24.1M01 Light Chain
  • Major capsid protein L1
KeywordsIMMUNE SYSTEM / HPV / antibody
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 speciesHuman papillomavirus 16
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsHurlburt, N.K. / Singh, S. / Rodarte, J.V. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: HPV16 neutralizing monoclonal antibodies show evidence for common developmental pathways and public epitopes
Authors: Carter, J.J. / Hurlburt, N.K.
History
DepositionDec 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 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

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Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
H: D24.1M01 Heavy Chain
L: D24.1M01 Light Chain
M: D24.1M01 Heavy Chain
N: D24.1M01 Light Chain
O: D24.1M01 Heavy Chain
P: D24.1M01 Light Chain
Q: D24.1M01 Heavy Chain
R: D24.1M01 Light Chain
S: D24.1M01 Heavy Chain
T: D24.1M01 Light Chain


Theoretical massNumber of molelcules
Total (without water)479,46815
Polymers479,46815
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

#1: Protein
Major capsid protein L1


Mass: 47492.496 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus 16 / Gene: L1 / Production host: Escherichia coli (E. coli) / Strain (production host): pLysS / References: UniProt: A0A161GYK1
#2: Antibody
D24.1M01 Heavy Chain


Mass: 25534.828 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#3: Antibody
D24.1M01 Light Chain


Mass: 22866.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
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: HPV16 L1 pentamer bound to five D24.1M01 Fabs / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.48 MDaYES
210.05 MDaYES
Source (natural)Organism: Human papillomavirus 16
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188743 / Symmetry type: POINT

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