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- PDB-3j8v: Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab -

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Basic information

Entry
Database: PDB / ID: 3j8v
TitleCryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab
Components
  • H16.14J heavy chain
  • H16.14J 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 / structural molecule activity / virion attachment to host cell
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: 13.9 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

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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-6121
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  • Superimposition on EM map
  • EMDB-6121
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.14J light chain
H: H16.14J heavy chain
J: H16.14J light chain
F: H16.14J heavy chain
K: H16.14J light chain
G: H16.14J heavy chain
M: H16.14J light chain
I: H16.14J heavy chain


Theoretical massNumber of molelcules
Total (without water)353,58613
Polymers353,58613
Non-polymers00
Water0
1
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.14J light chain
H: H16.14J heavy chain
J: H16.14J light chain
F: H16.14J heavy chain
K: H16.14J light chain
G: H16.14J heavy chain
M: H16.14J light chain
I: H16.14J heavy chain
x 60


Theoretical massNumber of molelcules
Total (without water)21,215,140780
Polymers21,215,140780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.14J light chain
H: H16.14J heavy chain
J: H16.14J light chain
F: H16.14J heavy chain
K: H16.14J light chain
G: H16.14J heavy chain
M: H16.14J light chain
I: H16.14J heavy chain
x 5


  • icosahedral pentamer
  • 1.77 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,767,92865
Polymers1,767,92865
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: L1
B: L1
C: L1
D: L1
E: L1
L: H16.14J light chain
H: H16.14J heavy chain
J: H16.14J light chain
F: H16.14J heavy chain
K: H16.14J light chain
G: H16.14J heavy chain
M: H16.14J light chain
I: H16.14J heavy chain
x 6


  • icosahedral 23 hexamer
  • 2.12 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,121,51478
Polymers2,121,51478
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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
H16.14J light chain


Mass: 11810.232 Da / Num. of mol.: 4 / Fragment: variable domain Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
H16.14J heavy chain


Mass: 12994.408 Da / Num. of mol.: 4 / Fragment: variable domain Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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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
IDNameTypeDetailsParent-ID
1Quasi-human papillomavirus 16 complexed with H16.14J FabCOMPLEX300 H16.14J Fabs bind to one HPV16 capsid0
2Human papillomavirus 16PapillomaviridaeVIRUS1
3H16.14J 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 mM Tris / pH: 7.4 / Details: 1 M NaCl, 200 mM Tris
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon support grid
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 102 K / Humidity: 90 %
Details: Blot for 0.7 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3)
Method: Blot for 0.7 seconds before plunging.

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Electron microscopy imaging

MicroscopyModel: JEOL 2100 / Date: Aug 27, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 4690 nm / Nominal defocus min: 620 nm / Cs: 2 mm / Camera length: 0 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: 385
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3Auto3DEM3D reconstruction
4EMAN23D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common Lines / Resolution: 13.9 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 5642 / Nominal pixel size: 2.33 Å / Actual pixel size: 2.33 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 necessary to perform contrast transfer function (CTF) correction for the extracted particles were assessed using Robem. The icosahedrally averaged reconstruction was initiated using a random model generated with setup_rmc. For the last step of refinement, the final maps were CTF-corrected using a B factor of 200 A2. (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
13OAE

3oae
PDB Unreleased entry

A1
23OAE

3oae
PDB Unreleased entry

B1
33OAE

3oae
PDB Unreleased entry

C1
43OAE

3oae
PDB Unreleased entry

D1
53OAE

3oae
PDB Unreleased entry

E1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms23594 0 0 0 23594

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