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- EMDB-20218: CryoEM structure of human papillomavirus 16 pseudovirus in comple... -

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Entry
Database: EMDB / ID: EMD-20218
TitleCryoEM structure of human papillomavirus 16 pseudovirus in complex human alpha-defensin 5 (HD5)
Map dataCryoEM structure of human papillomavirus 16 pseudovirus in complex with human alpha-defensin 5 (HD5)
Sample
  • Complex: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5)
    • Complex: alpha-defensin 5 (HD5)
    • Virus: Human papillomavirus type 16
Biological speciesHomo sapiens (human) / Human papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsGulati NM / Wiens ME / Smith JG / Stewart PL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01-AI104920 United States
CitationJournal: Pathog Immun / Year: 2019
Title: α-Defensin HD5 Stabilizes Capsid/Core Interactions.
Authors: Neetu M Gulati / Masaru Miyagi / Mayim E Wiens / Jason G Smith / Phoebe L Stewart /
Abstract: BACKGROUND: (HPV) is linked to nearly all cases of cervical cancer. Despite available vaccines, a deeper understanding of the immune response to HPV is needed. Human α-defensin 5 (HD5), an innate ...BACKGROUND: (HPV) is linked to nearly all cases of cervical cancer. Despite available vaccines, a deeper understanding of the immune response to HPV is needed. Human α-defensin 5 (HD5), an innate immune effector peptide, blocks infection of multiple sero-types of HPV, including high-risk HPV16. While a common mechanism of α-defensin anti-viral activity against nonenveloped viruses such as HPV has emerged, there is limited understanding of how α-defensins bind to viral capsids to block infection.
METHODS: We have used cryo-electron microscopy (cryoEM), mass spectrometry (MS) crosslinking and differential lysine modification studies, and molecular dynamics (MD) simulations to probe the ...METHODS: We have used cryo-electron microscopy (cryoEM), mass spectrometry (MS) crosslinking and differential lysine modification studies, and molecular dynamics (MD) simulations to probe the interaction of HPV16 pseudovirions (PsVs) with HD5.
RESULTS: CryoEM single particle reconstruction did not reveal HD5 density on the capsid surface. Rather, increased density was observed under the capsid shell in the presence of HD5. MS studies ...RESULTS: CryoEM single particle reconstruction did not reveal HD5 density on the capsid surface. Rather, increased density was observed under the capsid shell in the presence of HD5. MS studies indicate that HD5 binds near the L1 and L2 capsid proteins and specifically near the C-terminal region of L1. MD simulations indicate that favorable electrostatic interactions can be formed between HD5 and the L1 C-terminal tail.
CONCLUSIONS: A model is presented for how HD5 affects HPV16 structure and cell entry. In this model, HD5 binds to disordered regions of L1 and L2 protruding from the icosahedrally ordered capsid. HD5 ...CONCLUSIONS: A model is presented for how HD5 affects HPV16 structure and cell entry. In this model, HD5 binds to disordered regions of L1 and L2 protruding from the icosahedrally ordered capsid. HD5 acts to cement interactions between L1 and L2 and leads to a closer association of the L2/genome core with the L1 capsid. This model provides a structural rationale for our prior observation that HD5 interferes with the separation of L1 from the L2/genome complex during cell entry.
History
DepositionMay 13, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseSep 25, 2019-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20218.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of human papillomavirus 16 pseudovirus in complex with human alpha-defensin 5 (HD5)
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.08
Minimum - Maximum-0.12733757 - 0.27827927
Average (Standard dev.)0.0005827095 (±0.024572708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin100100100
Dimensions600600600
Spacing600600600
CellA=B=C: 756.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z756.000756.000756.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS100100100
NC/NR/NS600600600
D min/max/mean-0.1270.2780.001

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Supplemental data

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Sample components

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Entire : Complex of human papillomavirus type 16 pseudovirus with human al...

EntireName: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5)
Components
  • Complex: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5)
    • Complex: alpha-defensin 5 (HD5)
    • Virus: Human papillomavirus type 16

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Supramolecule #1: Complex of human papillomavirus type 16 pseudovirus with human al...

SupramoleculeName: Complex of human papillomavirus type 16 pseudovirus with human alpha-defensin 5 (HD5)
type: complex / ID: 1 / Parent: 0

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Supramolecule #3: alpha-defensin 5 (HD5)

SupramoleculeName: alpha-defensin 5 (HD5) / type: complex / ID: 3 / Parent: 1
Details: Synthesized linear HD5 peptide (CPC Scientific, Sunnyvale, CA) was subjected to thiol-disulfide reshuffling and purified to homogeneity by reverse-phase high-pressure liquid chromatography
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Sci species strain: pseudovirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: 293TT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1742
FSC plot (resolution estimation)

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