[English] 日本語
Yorodumi
- EMDB-7543: Structure of Zika virus at a resolution of 3.1 Angstrom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7543
TitleStructure of Zika virus at a resolution of 3.1 Angstrom
Map data
SampleZika virus:
virus / E protein / M protein / ligand
Function / homology
Function and homology information


suppression by virus of host TYK2 activity / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm ...suppression by virus of host TYK2 activity / flavivirin / methyltransferase cap1 / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host STAT1 activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / suppression by virus of host type I interferon-mediated signaling pathway / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / viral capsid / induction by virus of host autophagy / RNA-directed RNA polymerase / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / RNA helicase activity / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / serine-type endopeptidase activity / structural molecule activity / integral component of membrane / extracellular region / ATP binding / metal ion binding
DEAD box, Flavivirus / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A ...DEAD box, Flavivirus / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2A / Flavivirus glycoprotein central and dimerisation domain / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / 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 / Immunoglobulin E-set / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / mRNA cap 0/1 methyltransferase / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus capsid protein C superfamily / P-loop containing nucleoside triphosphate hydrolase
Genome polyprotein
Biological speciesZika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 / isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSevvana M / Long F / Miller AJ / Klose T / Buda G / Sun L / Kuhn RJ / Rossmann MR
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI076331 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI073755 United States
Citation
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 ReportPDB-ID: 6co8

SummaryFull reportAbout validation report
History
DepositionMar 12, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseJul 4, 2018-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6co8
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6co8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_7543.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 1024 pix.
= 829.44 Å
0.81 Å/pix.
x 1024 pix.
= 829.44 Å
0.81 Å/pix.
x 1024 pix.
= 829.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 3 / Movie #1: 3
Minimum - Maximum-25.904066 - 50.38329
Average (Standard dev.)0.10156658 (±1.5000882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-512-512-512
Dimensions102410241024
Spacing102410241024
CellA=B=C: 829.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.810.810.81
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z829.440829.440829.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-512-512-512
NC/NR/NS102410241024
D min/max/mean-25.90450.3830.102

-
Supplemental data

-
Additional map: ZIKV, unmasked half map - even

Fileemd_7543_additional_1.map
AnnotationZIKV, unmasked half map - even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: ZIKV, unmasked half map - odd

Fileemd_7543_additional_2.map
AnnotationZIKV, unmasked half map - odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: ZIKV, masked half map - even

Fileemd_7543_half_map_1.map
AnnotationZIKV, masked half map - even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: ZIKV, masked half map - odd

Fileemd_7543_half_map_2.map
AnnotationZIKV, masked half map - odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire Zika virus

EntireName: Zika virus / Number of components: 4

-
Component #1: virus, Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013

VirusName: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: 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

ProteinName: E protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 54.444051 kDa
SourceSpecies: isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)

-
Component #3: protein, M protein

ProteinName: M protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 8.496883 kDa
SourceSpecies: isolate ZIKV/Human/French Polynesia/10087PF/2013 (virus)

-
Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL
Buffer solution: 12 mM Tris-HCl, pH 8, 120 mM NaCl, 1 mM EDTA
pH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 33.3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000.0 X (nominal), 30864.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (100.0 - K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2085 / Sampling size: 5 µm

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 35842
3D reconstructionSoftware: jspr / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Soft mask was applied to the even/odd map before FSC calculation.
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Details: Real space followed by reciprocal space
Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

-
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
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

Read more

-
Yorodumi

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

Read more