+Open data
-Basic information
Entry | Database: PDB / ID: 3j8v | ||||||
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Title | Cryo-EM reconstruction of quasi-HPV16 complex with H16.14J Fab | ||||||
Components |
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Keywords | VIRUS/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 | ||||||
Biological species | Human papillomavirus type 16 Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.9 Å | ||||||
Authors | Guan, J. / Hafenstein, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j8v.cif.gz | 684.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j8v.ent.gz | 579.8 KB | Display | PDB format |
PDBx/mmJSON format | 3j8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j8v_validation.pdf.gz | 817.5 KB | Display | wwPDB validaton report |
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Full document | 3j8v_full_validation.pdf.gz | 906.1 KB | Display | |
Data in XML | 3j8v_validation.xml.gz | 88.6 KB | Display | |
Data in CIF | 3j8v_validation.cif.gz | 130.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8v ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8v | HTTPS FTP |
-Related structure data
Related structure data | 6121MC 5990C 6184C 3j8wC 3j8zC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | 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 | 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 | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 44.7 MDa / Experimental value: NO | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: OTHER / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||||||||||
Buffer solution | Name: 1 M NaCl, 200 mM Tris / pH: 7.4 / Details: 1 M NaCl, 200 mM Tris | ||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: glow-discharged holey carbon support grid | ||||||||||||||||||||
Vitrification | Instrument: 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. |
-Electron microscopy imaging
Microscopy | Model: JEOL 2100 / Date: Aug 27, 2014 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 4690 nm / Nominal defocus min: 620 nm / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 385 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Each particle | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Method: 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 building | Protocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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