+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27272 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of Western equine encephalitis virus VLP | |||||||||
Map data | Map of WEEV-VLP asymmetric unit | |||||||||
Sample |
| |||||||||
Keywords | WEEV / Alphavirus / VLP / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structural Genomics of Infectious Diseases / CSGID / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Western equine encephalitis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.35 Å | |||||||||
Authors | Zimmerman MI / Fremont DH | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Alternate repeat domain usage in an alphavirus entry receptor enables host species expansion Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C ...Authors: Zimmerman O / Zimmerman MI / Nelson CA / Raju S / Errico JM / Madden EA / Hassan AO / VanBlargan LA / Kim AS / Adams LJ / Basore K / Whitener BM / Earnest JT / Holmes AC / Ebel GD / Zmasek C / Scheuermann RH / Fremont DH / Diamond MS | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_27272.map.gz | 2.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-27272-v30.xml emd-27272.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_27272.png | 64.2 KB | ||
Filedesc metadata | emd-27272.cif.gz | 5.9 KB | ||
Others | emd_27272_half_map_1.map.gz emd_27272_half_map_2.map.gz | 77.8 MB 77.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27272 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27272 | HTTPS FTP |
-Related structure data
Related structure data | 8daqMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_27272.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Map of WEEV-VLP asymmetric unit | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half-map A
File | emd_27272_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half-map B
File | emd_27272_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half-map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Western equine encephalitis virus
Entire | Name: Western equine encephalitis virus |
---|---|
Components |
|
-Supramolecule #1: Western equine encephalitis virus
Supramolecule | Name: Western equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 11039 / Sci species name: Western equine encephalitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes |
---|
-Macromolecule #1: E1 envelope glycoprotein
Macromolecule | Name: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Western equine encephalitis virus |
Molecular weight | Theoretical: 47.188562 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA ...String: FEHATTVPNV PGIPYKALVE RAGYAPLNLE ITVVSSELTP STNKEYVTCK FHTVVPSPQV KCCGSLECKA SSKADYTCRV FGGVYPFMW GGAQCFCDSE NTQLSEAYVE FAPDCTIDHA VALKVHTAAL KVGLRIVYGN TTARLDTFVN GVTPGSSRDL K VIAGPISA AFSPFDHKVV IRKGLVYNYD FPEYGAMNPG AFGDIQASSL DATDIVARTD IRLLKPSVKN IHVPYTQAVS GY EMWKNNS GRPLQETAPF GCKIEVEPLR ATNCAYGHIP ISIDIPDAAF VRSSESPTIL EVSCTVADCI YSADFGGSLT LQY KANREG HCPVHSHSTT AVLKEATTHV TATGSITLHF STSSPQANFI VSLCGKKTTC NAECKPPADH IIGEPHKVDQ EFQA AVSKT SWNWLLALFG GASSLIVVGL IVLVCSSMLI NTR UniProtKB: Structural polyprotein |
-Macromolecule #2: E2 envelope glycoprotein
Macromolecule | Name: E2 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Western equine encephalitis virus |
Molecular weight | Theoretical: 46.171617 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH ...String: ITDDFTLTSP YLGFCPYCRH SAPCFSPIKI ENVWDESDDG SIRIQVSAQF GYNQAGTADV TKFRYMSYDH DHDIKEDSME KLAISTSGP CRRLGHKGYF LLAQCPPGDS VTVSITSGAS ENSCTVEKKI RRKFVGREEY LFPPVHGKLV KCHVYDHLKE T SAGYITMH RPGPHAYKSY LEEASGEVYI KPPSGKNVTY ECKCGDYSTG IVSTRTKMNG CTKAKQCIAY KRDQTKWVFN SP DLIRHTD HSVQGKLHIP FRLTPTVCPV PLAHTPTVTK WFKGITLHLT ATRPTLLTTR KLGLRADATA EWITGTTSRN FSV GREGLE YVWGNHEPVR VWAQESAPGD PHGWPHEIII HYYHRHPVYT VIVLCGVALA ILVGTASSAA CIAKARRDCL TPYA LAPNA TVPTALAVLC UniProtKB: Structural polyprotein |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.03 e/Å2 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 440062 |