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- PDB-3j8z: Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab -

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Basic information

Entry
Database: PDB / ID: 3j8z
TitleCryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab
Components
  • H16.1A heavy chain
  • H16.1A light chain
  • L1
KeywordsVIRUS/IMMUNE SYSTEM / L1 pentamer / quasi-HPV16 / L1 capsomer / Rosie online / VIRUS-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 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 16
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 14 Å
AuthorsGuan, J. / Hafenstein, S.
CitationJournal: Virology / Year: 2015
Title: Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals ...Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope. Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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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-5990
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.1A light chain
H: H16.1A heavy chain
J: H16.1A light chain
F: H16.1A heavy chain
K: H16.1A light chain
G: H16.1A heavy chain
M: H16.1A light chain
I: H16.1A heavy chain


Theoretical massNumber of molelcules
Total (without water)355,33113
Polymers355,33113
Non-polymers00
Water00
1
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.1A light chain
H: H16.1A heavy chain
J: H16.1A light chain
F: H16.1A heavy chain
K: H16.1A light chain
G: H16.1A heavy chain
M: H16.1A light chain
I: H16.1A heavy chain
x 60


Theoretical massNumber of molelcules
Total (without water)21,319,884780
Polymers21,319,884780
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: L1
B: L1
C: L1
D: L1
E: L1
L: H16.1A light chain
H: H16.1A heavy chain
J: H16.1A light chain
F: H16.1A heavy chain
K: H16.1A light chain
G: H16.1A heavy chain
M: H16.1A light chain
I: H16.1A heavy chain
x 5


  • icosahedral pentamer
  • 1.78 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,776,65765
Polymers1,776,65765
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.1A light chain
H: H16.1A heavy chain
J: H16.1A light chain
F: H16.1A heavy chain
K: H16.1A light chain
G: H16.1A heavy chain
M: H16.1A light chain
I: H16.1A heavy chain
x 6


  • icosahedral 23 hexamer
  • 2.13 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,131,98878
Polymers2,131,98878
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: Protein
L1 / L1 protein / Major capsid protein L1


Mass: 50873.422 Da / Num. of mol.: 5 / Fragment: UNP residues 47-500 / Source method: isolated from a natural source / Source: (natural) Human papillomavirus type 16 / References: UniProt: Q4VRM0, UniProt: P03101*PLUS
#2: Antibody
H16.1A light chain


Mass: 12637.040 Da / Num. of mol.: 4 / Fragment: variable domain Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
H16.1A heavy chain


Mass: 12604.032 Da / Num. of mol.: 4 / Fragment: variable domain Fab / 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
IDNameTypeParent-ID
1Quasi-HPV16 complex with Fab H16.1ACOMPLEX0
2Human papillomavirus 16VIRUS1
3H16.1A Fab1
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: Plunged into liquid ethane-propane mixture (FEI VITROBOT MARK III).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 9, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 50
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3Auto3DEM3D reconstruction
CTF correctionDetails: auto3dem
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: common lines / Resolution: 14 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2300 / Nominal pixel size: 1.3 Å / Actual pixel size: 1.3 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--flexible
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms23714 0 0 0 23714

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