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- EMDB-30414: Subparticle refinement of human papillomavirus type 16 pesudoviru... -

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Basic information

Entry
Database: EMDB / ID: EMD-30414
TitleSubparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
Map dataSub-particle reconstruction of the 2-fold region of the cryo-EM structure of HPV16 pseudovirus complexed with H16.001 Fab
Sample
  • Complex: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
    • Protein or peptide: The light chain variable region of H16.001 Fab fragment
    • Protein or peptide: The heavy chain variable region of H16.001 Fab fragment
    • Protein or peptide: Major capsid protein L1
KeywordsVirus / immune complex / IMMUNE SYSTEM-VIRAL PROTEIN 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
Similarity search - Component
Biological speciesHuman papillomavirus type 16 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsHe MZ / Li SW
CitationJournal: NPJ Vaccines / Year: 2020
Title: Structural characterization of a neutralizing mAb H16.001, a potent candidate for a common potency assay for various HPV16 VLPs.
Authors: Weijin Huang / Maozhou He / Tingting Ning / Jianhui Nie / Feng Zhang / Qingbing Zheng / Rui Zhang / Ying Xu / Ying Gu / Shaowei Li / Youchun Wang /
Abstract: With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different ...With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different expression systems and bioprocesses is urgently needed for the potency characterization. Among all mAbs against HPV16 collected, rabbit mAb H16.001 is potently neutralizing with the highest affinity, recognizes an immune-dominant epitope, and can comparably react with HPV16 vaccines from various sources. Cryo-electron microscopic (cryo-EM) structure demonstrated that 360 H16.001 Fabs could bind to HPV16 capsid in preferable binding manner without steric hindrance between neighboring Fabs, potentially supporting its identification for VLP structural integrity and utility in monitoring VLP structural probity. This structural analysis indicated that mAb H16.001 afforded unbiased potency characterization for various HPV16 vaccines and was potential for use in vaccine regulation practice. This study also showed a model process for selecting suitable mAbs for potency assays of other vaccines.
History
DepositionJul 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cn2
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cn2
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30414.png

Downloads & links

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Map

FileDownload / File: emd_30414.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-particle reconstruction of the 2-fold region of the cryo-EM structure of HPV16 pseudovirus complexed with H16.001 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 768 pix.
= 866.304 Å		1.13 Å/pix.
x 768 pix.
= 866.304 Å		1.13 Å/pix.
x 768 pix.
= 866.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-11.804463 - 17.826657999999998
Average (Standard dev.)0.0026609353 (±0.43449277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 866.304 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z866.304866.304866.304
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS768768768
D min/max/mean-11.80417.8270.003

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Supplemental data

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Sample components

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Entire : human papillomavirus type 16 pesudovirus in complex with H16.001 Fab

EntireName: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
Components
  • Complex: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
    • Protein or peptide: The light chain variable region of H16.001 Fab fragment
    • Protein or peptide: The heavy chain variable region of H16.001 Fab fragment
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab

SupramoleculeName: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human papillomavirus type 16

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Macromolecule #1: The light chain variable region of H16.001 Fab fragment

MacromoleculeName: The light chain variable region of H16.001 Fab fragment
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.50979 KDa
SequenceString:
DPMLTQTAAS VEVAVGGTVT IKCQASQSIG GYLSWYQQKP GQRPKLLIYR ASTLASGVPS RFKGSGSGTE YTLTFSGVEC ADAAAYYCQ QGYTSSDINN AFGGGTEVVV K

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Macromolecule #2: The heavy chain variable region of H16.001 Fab fragment

MacromoleculeName: The heavy chain variable region of H16.001 Fab fragment
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 13.212764 KDa
SequenceString:
QSVKESEGRL VTPGTPLTLT CTASGFTMSR YHMTWVRQAP GKGLEWIGII YARNSDTYYA NWAKGRFTIS KTSTTVDLKI TSPTIEDTA TYFCARVDSD SSGAFDRLDL WGQGTLVTVS S

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Macromolecule #3: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus type 16
Molecular weightTheoretical: 56.340953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH ...String:
MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH WGKGSPCTNV AVNPGDCPPL ELINTVIQDG DMVDTGFGAM DFTTLQANKS EVPLDICTSI CKYPDYIKMV SE PYGDSLF FYLRREQMFV RHLFNRAGAV GENVPDDLYI KGSGSTANLA SSNYFPTPSG SMVTSDAQIF NKPYWLQRAQ GHN NGICWG NQLFVTVVDT TRSTNMSLCA AISTSETTYK NTNFKEYLRH GEEYDLQFIF QLCKITLTAD VMTYIHSMNS TILE DWNFG LQPPPGGTLE DTYRFVTSQA IACQKHTPPA PKEDPLKKYT FWEVNLKEKF SADLDQFPLG RKFLLQAGLK AKPKF TLGK RKATPTTSST STTAKRKKRK L

UniProtKB: Major capsid protein L1

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 274860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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