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- EMDB-8147: Cryo-EM structure of Human Papillomavirus Type 59 L1 Virus-like P... -

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Basic information

Entry
Database: EMDB / ID: EMD-8147
TitleCryo-EM structure of Human Papillomavirus Type 59 L1 Virus-like Particle
Map dataNone
Sample
  • Virus: Human papillomavirus type 59
    • Protein or peptide: Major capsid protein L1
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
Similarity search - Component
Biological speciesHuman papillomavirus type 59
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsLi ZH / Yan XD / Yu H / Zheng QB / Gu Y / Li SW
Funding support China, United States, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation81172885 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM33050 United States
CitationJournal: Structure / Year: 2016
Title: The C-Terminal Arm of the Human Papillomavirus Major Capsid Protein Is Immunogenic and Involved in Virus-Host Interaction.
Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni ...Authors: Zhihai Li / Xiaodong Yan / Hai Yu / Daning Wang / Shuo Song / Yunbing Li / Maozhou He / Qiyang Hong / Qingbing Zheng / Qinjian Zhao / Ying Gu / Jun Zhang / Mandy E W Janssen / Giovanni Cardone / Norman H Olson / Timothy S Baker / Shaowei Li / Ningshao Xia /
Abstract: Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial ...Cervical cancer is the second most prevalent malignant tumor among women worldwide. High-risk human papillomaviruses (HPVs) are believed to be the major causative pathogens of mucosal epithelial cancers including cervical cancer. The HPV capsid is made up of 360 copies of major (L1) and 72 copies of minor (L2) capsid proteins. To date, limited high-resolution structural information about the HPV capsid has hindered attempts to understand details concerning the mechanisms by which HPV assembles and infects cells. In this study, we have constructed a pseudo-atomic model of the HPV59 L1-only capsid and demonstrate that the C-terminal arm of L1 participates in virus-host interactions. Moreover, when conjugated to a scaffold protein, keyhole limpet hemocyanin (KLH), this arm is immunogenic in vivo. These results provide new insights that will help elucidate HPV biology, and hence pave a way for the design of next-generation HPV vaccines.
History
DepositionApr 22, 2016-
Header (metadata) releaseMay 18, 2016-
Map releaseMay 18, 2016-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.25
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jb1
  • Surface level: 4.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jb1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8147.png

Downloads & links

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Map

FileDownload / File: emd_8147.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 4.25 / Movie #1: 4.25
Minimum - Maximum-6.758176 - 14.132822
Average (Standard dev.)-1.0509302e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-410-410-410
Dimensions820820820
Spacing820820820
CellA=B=C: 910.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z820820820
origin x/y/z0.0000.0000.000
length x/y/z910.200910.200910.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-410-410-410
NC/NR/NS820820820
D min/max/mean-6.75814.133-0.000

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Supplemental data

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Sample components

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Entire : Human papillomavirus type 59

EntireName: Human papillomavirus type 59
Components
  • Virus: Human papillomavirus type 59
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Human papillomavirus type 59

SupramoleculeName: Human papillomavirus type 59 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37115 / Sci species name: Human papillomavirus type 59 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Escherichia coli (E. coli) / Recombinant strain: ER2566 / Recombinant plasmid: pTO-T7
Molecular weightTheoretical: 19.8 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 580.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus type 59
Molecular weightTheoretical: 55.978418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKVYLPPPSV AKVVSTDEYV TRTSIFYHAG SSRLLTVGHP YFKVPKGGNG RQDVPKVSAY QYRVFRVKLP DPNKFGLPDN TVYDPNSQR LVWACVGVEI GRGQPLGVGL SGHPLYNKLD DTENSHVASA VDTKDTRDNV SVDYKQTQLC IIGCVPAIGE H WTKGTACK ...String:
MKVYLPPPSV AKVVSTDEYV TRTSIFYHAG SSRLLTVGHP YFKVPKGGNG RQDVPKVSAY QYRVFRVKLP DPNKFGLPDN TVYDPNSQR LVWACVGVEI GRGQPLGVGL SGHPLYNKLD DTENSHVASA VDTKDTRDNV SVDYKQTQLC IIGCVPAIGE H WTKGTACK PTTVVQGDCP PLELINTPIE DGDMVDTGYG AMDFKLLQDN KSEVPLDICQ SICKYPDYLQ MSADAYGDSM FF CLRREQV FARHFWNRSG TMGDQLPESL YIKGTDIRAN PGSYLYSPSP SGSVVTSDSQ LFNKPYWLHK AQGLNNGICW HNQ LFLTVV DTTRSTNLSV CASTTSSIPN VYTPTSFKEY ARHVEEFDLQ FIFQLCKITL TTEVMSYIHN MNTTILEDWN FGVT PPPTA SLVDTYRFVQ SAAVTCQKDT APPVKQDPYD KLKFWPVDLK ERFSADLDQF PLGRKFLLQL GARPKPTIGP RKRAA PAPT STPSPKRVKR RKSSRK

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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

Concentration5 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
8.0 mg/mLNaClSodium chloridesodium chloride
0.2 mg/mLKClpotassium chloride
1.42 mg/mLNa2HPO4Disodium phosphate
0.24 mg/mLKH2PO4Monopotassium phosphate
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: ctffind3
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: Auto3DEM (ver. 4.05)
Details: The effective resolution was estimated based on the 0.5 criteria of FSC between the cryoEM structure and the final model derived from the density map.
Number images used: 3100

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-5jb1:
Pseudo-atomic structure of Human Papillomavirus Type 59 L1 Virus-like Particle

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