|Entry||Database: EMDB / ID: 7543|
|Title||Structure of Zika virus at a resolution of 3.1 Angstrom|
|Map data||ZIKV map at resolution of 3.1 Angstrom|
virus / E protein / M protein / ligand
|Function / homology||Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain ...Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus non-structural protein NS4A / mRNA cap 0 and cap 1 methyltransferase (EC 184.108.40.206 and EC 220.127.116.11) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus polyprotein propeptide / Flavivirus non-structural protein NS4B / Flaviviral glycoprotein E, dimerisation domain / Flavivirus non-structural protein NS2A / Flavivirus envelope glycoprotein M / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus non-structural Protein NS1 / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / suppression by virus of host TYK2 activity / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / host cell perinuclear region of cytoplasm / RNA helicase activity / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / 4 iron, 4 sulfur cluster binding / RNA helicase / nucleoside-triphosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / GTP binding / virion membrane / structural molecule activity / serine-type endopeptidase activity / regulation of transcription, DNA-templated / transcription, DNA-templated / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein|
Function and homology information
|Source||Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 / isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)|
|Method||single particle reconstruction / cryo EM / 3.1 Å resolution|
|Authors||Sevvana M / Long F / Miller AJ / Klose T / Buda G / Sun L / Kuhn RJ / Rossmann MR|
Journal: Structure / Year: 2018
Title: Refinement and Analysis of the Mature Zika Virus Cryo-EM Structure at 3.1 Å Resolution.
Authors: Madhumati Sevvana / Feng Long / Andrew S Miller / Thomas Klose / Geeta Buda / Lei Sun / Richard J Kuhn / Michael G Rossmann
Abstract: Among the several arthropod-borne human flaviviral diseases, the recent outbreak of Zika virus (ZIKV) has caused devastating birth defects and neurological disorders, challenging the world with ...Among the several arthropod-borne human flaviviral diseases, the recent outbreak of Zika virus (ZIKV) has caused devastating birth defects and neurological disorders, challenging the world with another major public health concern. We report here the refined structure of the mature ZIKV at a resolution of 3.1 Å as determined by cryo-electron microscopic single-particle reconstruction. The improvement in the resolution, compared with previous enveloped virus structures, was the result of optimized virus preparation methods and data processing techniques. The glycoprotein interactions and surface properties of ZIKV were compared with other mosquito-borne flavivirus structures. The largest structural differences and sequence variations occur at the glycosylation loop associated with receptor binding. Probable drug binding pockets were identified on the viral surface. These results also provide a structural basis for the design of vaccines against ZIKV.
#1: Journal: Science / Year: 2016
Title: The 3.8 Å resolution cryo-EM structure of Zika virus.
Authors: Devika Sirohi / Zhenguo Chen / Lei Sun / Thomas Klose / Theodore C Pierson / Michael G Rossmann / Richard J Kuhn
Abstract: The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, ...The recent rapid spread of Zika virus and its unexpected linkage to birth defects and an autoimmune neurological syndrome have generated worldwide concern. Zika virus is a flavivirus like the dengue, yellow fever, and West Nile viruses. We present the 3.8 angstrom resolution structure of mature Zika virus, determined by cryo-electron microscopy (cryo-EM). The structure of Zika virus is similar to other known flavivirus structures, except for the ~10 amino acids that surround the Asn(154) glycosylation site in each of the 180 envelope glycoproteins that make up the icosahedral shell. The carbohydrate moiety associated with this residue, which is recognizable in the cryo-EM electron density, may function as an attachment site of the virus to host cells. This region varies not only among Zika virus strains but also in other flaviviruses, which suggests that differences in this region may influence virus transmission and disease.
|Validation Report||PDB-ID: 6co8|
SummaryFull reportAbout validation report
|Date||Deposition: Mar 12, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Jul 4, 2018 / Last update: Jul 11, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7543.map.gz (map file in CCP4 format, 4294968 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 0.81 Å|
CCP4 map header:
-Entire Zika virus
|Entire||Name: Zika virus / Number of components: 4|
-Component #1: virus, Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
|Virus||Name: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013|
Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
|Species||Species: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013|
Strain: ZIKV/Human/French Polynesia/10087PF/2013
|Source (natural)||Host Species: Homo sapiens (human)|
-Component #2: protein, E protein
|Protein||Name: E protein / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 54.444051 kDa|
|Source||Species: isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)|
-Component #3: protein, M protein
|Protein||Name: M protein / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 8.496883 kDa|
|Source||Species: isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)|
-Component #4: ligand, N-ACETYL-D-GLUCOSAMINE
|Ligand||Name: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 0.221208 kDa|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/ml|
Buffer solution: 12 mM Tris-HCl, pH 8, 120 mM NaCl, 1 mM EDTA
|Vitrification||Cryogen name: ETHANE|
-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: 33.3 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 18000. X (nominal), 30864. X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 100.0 - K)|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2085 / Sampling size: 5 microns|
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Refinement space: REAL / Details: Real space followed by reciprocal space|
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
-Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi