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- PDB-9vz8: Local refinement region of HPV45 in complex with antibody 10G2 -

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Basic information

Entry
Database: PDB / ID: 9vz8
TitleLocal refinement region of HPV45 in complex with antibody 10G2
Components
  • 10G2 Fab heavy chain
  • 10G2 Fab light chain
  • Major capsid protein L1
KeywordsVIRUS LIKE PARTICLE / Human papillomavirus / Cryo-EM / structural protein
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 45
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsJiang, Y. / Sun, H. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of human papillomavirus type 45 in complexed with the Fab fragment of 10G2
Authors: Jiang, Y. / Sun, H. / Wang, Z. / Zheng, Q. / Li, S. / Xia, N.
History
DepositionJul 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data 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
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
L: 10G2 Fab light chain
H: 10G2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)197,7215
Polymers197,7215
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: Protein Major capsid protein L1


Mass: 57379.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human papillomavirus 45 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P36741
#2: Antibody 10G2 Fab light chain


Mass: 12215.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 10G2 Fab heavy chain


Mass: 13365.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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
1Local refinement region of HPV45 in complex with antibody 10G2COMPLEXall0MULTIPLE SOURCES
2Human papillomavirus type 45COMPLEX#11RECOMBINANT
3The Fab fragment of 10G2COMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22human papillomavirus 4510593
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Homo sapiens (human)9606
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20_4459model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 993420 / Symmetry type: POINT
RefinementHighest resolution: 3.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047843
ELECTRON MICROSCOPYf_angle_d0.56510697
ELECTRON MICROSCOPYf_dihedral_angle_d4.1161076
ELECTRON MICROSCOPYf_chiral_restr0.0441184
ELECTRON MICROSCOPYf_plane_restr0.0061370

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