+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Bufavirus 1 at pH 2.6 | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Bufavirus / parvovirus / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Phospholipase A2-like domain / Phospholipase A2-like domain / 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 / VP1![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
![]() | Gulkis MC / McKenna R / Bennett AD | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural Characterization of Human Bufavirus 1: Receptor Binding and Endosomal pH-Induced Changes Authors: Gulkis M / Luo M / Chipman P / Mietzsch M / Soderlund-Venermo M / Bennett A / McKenna R | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 194.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.4 KB | Display | ![]() |
Images | ![]() | 97.8 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() | 364.4 MB 364.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9cws ![]() 45954 ![]() 45955 ![]() 45958 M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_45973_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_45973_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Bufavirus-1
Entire | Name: ![]() |
---|---|
Components |
|
-Supramolecule #1: Bufavirus-1
Supramolecule | Name: Bufavirus-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Bufavirus 1 VP2 was overexpressed in Sf9 cells / NCBI-ID: 1209382 / Sci species name: Bufavirus-1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
---|---|
Host (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4 MDa |
Virus shell | Shell ID: 1 / Diameter: 260.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 80.543203 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPAIRKARGW VPPGYNYLGP FNQDFNKKPT NPSDNAARKH DLEYNKLIKQ GHNPYWNYNH ADEDFIKETD QATDWGGKFG NFVFRAKRA LAPELAPPAK KKTKTKHTEP EYSHKHIKAG TKRGKPFYLF VNLARKKARM TDTQDVSEQQ SDQPSVASTN A KAGGGGGG ...String: MPAIRKARGW VPPGYNYLGP FNQDFNKKPT NPSDNAARKH DLEYNKLIKQ GHNPYWNYNH ADEDFIKETD QATDWGGKFG NFVFRAKRA LAPELAPPAK KKTKTKHTEP EYSHKHIKAG TKRGKPFYLF VNLARKKARM TDTQDVSEQQ SDQPSVASTN A KAGGGGGG GGSGVGHSTG NYNNRTEFYY HGDEVTIVCH SSRHIHLNMS ESEEYKIYDT DRGPRFPTDQ TLQGRDTIND SY HAQVETP WFLINPNSWG TWMNPADFQQ LTTTCREVTL EHLDQTLDNI VIKTVSKQGS GAEETTQYNN DLTALLQVAL DKS NQLPWV ADNMYLDSLG YIPWRPCKLK QYSYHVNFWN TIDIISGPQQ NQWQQVKKEI RWDDLQFTPI ETTTEIDLLR TGDS WTSGP YKFNTKPTQL SYHWQSTRHT GSVHPTDPPN AIGQQGQNIR DINGWQWGDR SDPMSAATRV SNFHIGYSWP EWRIH YGSG GPAINPGAPF SQAPWSTDPQ VRLTQGASEK AIFDYNHGDD DPAHRDQWWQ NNLPITGQTN WAPKNAHQAN LSSNVP SRQ EFWTQDYHNT FGPFTAVDDV GIQYPWGAIW TKTPDTTHKP MMSAHAPFIC KDGPPGQLLV KLAPNYTENL QTDGLGN NR IVTYATFWWT GKLILKGKLR LPRQFNLYNL PGRPRGTEAK KFLPNEIGHF ELPFMPGRCM PNYTM UniProtKB: VP1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.5 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| |||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Specialist optics | Energy filter - Slit width: 20 eV |
Software | Name: Leginon |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number real images: 1496 / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
---|---|
Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 166.7 / Target criteria: Cross-correlation coefficient |
Output model | ![]()
PDB-9cws: |