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- PDB-3j8w: Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab -

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Basic information

Entry
Database: PDB / ID: 3j8w
TitleCryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab
Components
  • H263.A2 heavy chain
  • H263.A2 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 / host cell nucleus / virion attachment to host cell / 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 speciesMus musculus (house mouse)
Human papillomavirus type 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 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 19, 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 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / 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 / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _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
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-6184
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  • Superimposition on EM map
  • EMDB-6184
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: H263.A2 light chain
H: H263.A2 heavy chain
J: H263.A2 light chain
F: H263.A2 heavy chain
K: H263.A2 light chain
G: H263.A2 heavy chain
M: H263.A2 light chain
I: H263.A2 heavy chain
A: L1
B: L1
C: L1
D: L1
E: L1


Theoretical massNumber of molelcules
Total (without water)354,59113
Polymers354,59113
Non-polymers00
Water00
1
L: H263.A2 light chain
H: H263.A2 heavy chain
J: H263.A2 light chain
F: H263.A2 heavy chain
K: H263.A2 light chain
G: H263.A2 heavy chain
M: H263.A2 light chain
I: H263.A2 heavy chain
A: L1
B: L1
C: L1
D: L1
E: L1
x 60


Theoretical massNumber of molelcules
Total (without water)21,275,445780
Polymers21,275,445780
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
L: H263.A2 light chain
H: H263.A2 heavy chain
J: H263.A2 light chain
F: H263.A2 heavy chain
K: H263.A2 light chain
G: H263.A2 heavy chain
M: H263.A2 light chain
I: H263.A2 heavy chain
A: L1
B: L1
C: L1
D: L1
E: L1
x 5


  • icosahedral pentamer
  • 1.77 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,772,95465
Polymers1,772,95465
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
L: H263.A2 light chain
H: H263.A2 heavy chain
J: H263.A2 light chain
F: H263.A2 heavy chain
K: H263.A2 light chain
G: H263.A2 heavy chain
M: H263.A2 light chain
I: H263.A2 heavy chain
A: L1
B: L1
C: L1
D: L1
E: L1
x 6


  • icosahedral 23 hexamer
  • 2.13 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,127,54578
Polymers2,127,54578
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
H263.A2 light chain


Mass: 11942.283 Da / Num. of mol.: 4 / Fragment: variable domain Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
H263.A2 heavy chain


Mass: 13113.628 Da / Num. of mol.: 4 / Fragment: variable domain Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: 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
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 complexed with H263.A2 FabsCOMPLEX0
2Human papillomavirus 16VIRUS1
3H263.A2 Fab1
Molecular weightValue: 44.7 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 1 M NaCl, 200 nM Tris / pH: 7.4 / Details: 1 M NaCl, 200 nM Tris
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon supported grid
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 102 K / Humidity: 90 % / Details: Plunged into liquid ethane (GATAN CRYOPLUNGE 3).

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Electron microscopy imaging

MicroscopyModel: JEOL 2100 / Date: Jul 31, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 5520 nm / Nominal defocus min: 1490 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 264
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: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common Lines / Resolution: 13 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 8908 / Nominal pixel size: 2.86 Å / Actual pixel size: 2.86 Å
Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images ...Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values used to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstruction was initiated using a random model generated with setup_rmc and reached 14 A resolution estimated at a Fourier Shell Correlation (FSC) of 0.5. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2. (Single particle details: The particles were selected using semi-automatic program e2boxer.py (EMAN2)) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building

3D fitting-ID: 1 / Accession code: 3OAE / Initial refinement model-ID: 1 / PDB-ID: 3OAE

3oae
PDB Unreleased entry

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2B
3C
4D
5E
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms23678 0 0 0 23678

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