+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-23105 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human Bocavirus 2 (pH 7.4) | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Icosahedral Capsid / Human Bocavirus 2 / HBoV2 / VIRUS / Parvovirus | |||||||||
Function / homology | Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.71 Å | |||||||||
![]() | Luo M / Mietzsch M | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: pH-Induced Conformational Changes of Human Bocavirus Capsids. Authors: Mengxiao Luo / Mario Mietzsch / Paul Chipman / Kangkang Song / Chen Xu / John Spear / Duncan Sousa / Robert McKenna / Maria Söderlund-Venermo / Mavis Agbandje-McKenna / ![]() ![]() Abstract: Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and ...Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid. Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a "basket" motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 323.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
Images | ![]() | 295.9 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l0vMC ![]() 7l0uC ![]() 7l0wC ![]() 7l0xC ![]() 7l0yC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.958 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Human bocavirus 2
Entire | Name: ![]() |
---|---|
Components |
|
-Supramolecule #1: Human bocavirus 2
Supramolecule | Name: Human bocavirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 573977 / Sci species name: Human bocavirus 2 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
---|
-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 57.591254 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSGVGISTGG WVGGSYFTDS YVITKNTRQF LVKIQNDHKY RTENIIPSNA GGKSQRCVST PWSYFNFNQY SSHFSPQDWQ RLTNEYKRF KPRKMHVKIY NLQIKQILSN GADTTYNNDL TAGVHIFCDG EHAYPNATHP WDEDVMPELP YETWYLFQYG Y IPVIHELA ...String: GSGVGISTGG WVGGSYFTDS YVITKNTRQF LVKIQNDHKY RTENIIPSNA GGKSQRCVST PWSYFNFNQY SSHFSPQDWQ RLTNEYKRF KPRKMHVKIY NLQIKQILSN GADTTYNNDL TAGVHIFCDG EHAYPNATHP WDEDVMPELP YETWYLFQYG Y IPVIHELA EMEDANAVEK AIALQIPFFM LENSDHEVLR TGESTEFTFD FDCEWINNER AYIPPGLMFN PKVPTRRAQY IR QHGNTAS SNTRIQPYAK PTSWMTGPGL LSAQRVGPAG SDTASWMVVV NPDGTAVNSG MAGVGSGFDP PSGSLRPTDL EYK IQWYQT PEGTNSDGNI ISNPPLSMLR DQALYRGNQT TYNLCSDVWM FPNQIWDRYP ITRENPIWCK KPRSDKNTII DPFD GTLAM DHPPGTIFIK MAKIPVPSNN NADSYLNIYC TGQVSCEIVW EVERYATKNW RPERRHTALG LGIGGEENIN PTYHV DKNG KYIQPTTWDM CYPIKTNINK VL UniProtKB: VP2 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: OTHER |
---|---|
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 188857 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |