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- PDB-6bt3: High-Resolution Structure Analysis of Antibody V5 Conformational ... -

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Basic information

Entry
Database: PDB / ID: 6bt3
TitleHigh-Resolution Structure Analysis of Antibody V5 Conformational Epitope on Human Papillomavirus 16
Components
  • Major capsid protein L1
  • V5 Fab Heavy-chain
  • V5 Fab Light-chain
KeywordsVIRUS / HPV16 / H16.V5 / Fab / VIRUS LIKE PARTICLE-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 speciesMus musculus (house mouse)
Human papillomavirus type 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsGuan, J. / Bywaters, S.M. / Brendle, S.A. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Christensen, N.D. / Hafenstein, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD019995 United States
CitationJournal: Viruses / Year: 2017
Title: High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic ...Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to maximize long-term protection against multiple types of HPV. Fragments of antibody (Fab) digested from the neutralizing monoclonal antibodies H16.V5 (V5) and H16.U4 (U4) were bound to HPV16 capsids and the structures of the two virus-Fab complexes were solved to near atomic resolution using cryo-electron microscopy. The structures reveal virus conformational changes, the Fab-binding mode to the capsid, the residues comprising the epitope and indicate a potential interaction of U4 with the minor structural protein, L2. Competition enzyme-linked immunosorbent assay (ELISA) showed V5 outcompetes U4 when added sequentially, demonstrating a steric interference even though the footprints do not overlap. Combined with our previously reported immunological and structural results, we propose that the virus may initiate host entry through an interaction between the icosahedral five-fold vertex of the capsid and receptors on the host cell. The highly detailed epitopes identified for the two antibodies provide a framework for continuing biochemical, genetic and biophysical studies.
History
DepositionDec 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_nat / Item: _entity_src_nat.common_name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8243
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)526,88014
Polymers526,88014
Non-polymers00
Water00
1
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)31,612,780840
Polymers31,612,780840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 2.63 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)2,634,39870
Polymers2,634,39870
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 3.16 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)3,161,27884
Polymers3,161,27884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Antibody
V5 Fab Light-chain


Mass: 23832.492 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
V5 Fab Heavy-chain


Mass: 23739.500 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein
Major capsid protein L1


Mass: 56098.617 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Human papillomavirus type 16 / References: UniProt: P03101
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 complexed with V5 Fab / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17612 / Symmetry type: POINT

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