|Entry||Database: EMDB / ID: EMD-23081|
|Title||High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility|
|Sample||Human papillomavirus type 16:|
virus / Major capsid protein L1
|Function / homology||Double-stranded DNA virus, group I, capsid / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / Major capsid protein L1|
Function and homology information
|Biological species||Human papillomavirus type 16|
|Method||single particle reconstruction / cryo EM / Resolution: 3.1 Å|
|Authors||Hartmann SR / Goetschius DJ / Hafenstein S|
|Funding support|| United States, 1 items |
|Citation||Journal: Sci Rep / Year: 2021|
Title: High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility.
Authors: Daniel J Goetschius / Samantha R Hartmann / Suriyasri Subramanian / Carol M Bator / Neil D Christensen / Susan L Hafenstein /
Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly associated with terminal keratinocyte ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly associated with terminal keratinocyte differentiation making production and purification of high titer virus preparations for research problematic, therefore alternative HPV production methods have been developed for virological and structural studies. In this study we use HPV16 quasivirus, composed of HPV16 L1/L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome. We have achieved the first high resolution, 3.1 Å, structure of HPV16 by using a local subvolume refinement approach. The high resolution enabled us to build L1 unambiguously and identify L2 protein strands. The L2 density is incorporated adjacent to conserved L1 residues on the interior of the capsid. Further interpretation with our own software for Icosahedral Subvolume Extraction and Correlated Classification revealed flexibility, on the whole-particle level through diameter analysis and local movement with inter-capsomer analysis. Inter-capsomer expansion or contraction, governed by the connecting arms, showed no bias in the magnitude or direction of capsomer movement. We propose that papillomavirus capsids are dynamic and capsomers move as rigid bodies connected by flexible linkers. The resulting virus structure will provide a framework for continuing biochemical, genetic and biophysical research for papillomaviruses. Furthermore, our approach has allowed insight into the resolution barrier that has previously been a limitation in papillomavirus structural studies.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_23081.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.1 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Additional map: HPV16 quasivirus pentavalent capsomer subvolume refinement.
|Annotation||HPV16 quasivirus pentavalent capsomer subvolume refinement.|
|Projections & Slices|
-Additional map: HPV16 quasivirus hexavalent capsomer subvolume refinement.
|Annotation||HPV16 quasivirus hexavalent capsomer subvolume refinement.|
|Projections & Slices|
-Additional map: HPV16 quasivirus icosahedral refinement from which pentavalent and...
-Entire Human papillomavirus type 16
|Entire||Name: Human papillomavirus type 16 / Number of components: 2|
-Component #1: virus, Human papillomavirus type 16
|Virus||Name: Human papillomavirus type 16 / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Human papillomavirus type 16|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: 293TT|
-Component #2: protein, Major capsid protein L1
|Protein||Name: Major capsid protein L1 / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 56.098617 kDa|
|Source||Species: Human papillomavirus type 16|
|Source (engineered)||Expression System: Homo sapiens (human)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 0.01 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON III (4k x 4k)|
|Image acquisition||Number of digital images: 10143|
|Processing||Method: single particle reconstruction / Number of projections: 181299|
|3D reconstruction||Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
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