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- PDB-6co8: Structure of Zika virus at a resolution of 3.1 Angstrom -

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Basic information

Entry
Database: PDB / ID: 6co8
TitleStructure of Zika virus at a resolution of 3.1 Angstrom
Components
  • E protein
  • M protein
KeywordsVIRUS / Zika / flavivirus
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
Flavivirus NS3, petidase S7 / RNA-directed RNA polymerase, flavivirus / 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 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus glycoprotein central and dimerisation domain ...Flavivirus NS3, petidase S7 / RNA-directed RNA polymerase, flavivirus / 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 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus glycoprotein central and dimerisation domain / Envelope glycoprotein M, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / DEAD box, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / Peptidase S1, PA clan / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein M / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus capsid protein C superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus envelope glycoprotein M-like / Monooxygenase - #260 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Monooxygenase / Helicase, Ruva Protein; domain 3 / Immunoglobulin-like / Up-down Bundle / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Genome polyprotein
Biological speciesZika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSevvana, M. / Long, F. / Miller, A.J. / Klose, T. / Buda, G. / Sun, L. / Kuhn, R.J. / Rossmann, M.R.
Funding support United States, 2items
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 Report
SummaryFull reportAbout validation report
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / em_entity_assembly_naturalsource / entity_src_nat
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_entity_assembly_naturalsource.organism / _entity_src_nat.pdbx_organism_scientific
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-7543
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  • Superimposition on EM map
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Movie viewer
Structure viewerMolecule:
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Assembly

Deposited unit
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,15012
Polymers188,8236
Non-polymers1,3276
Water0
1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)11,409,003720
Polymers11,329,368360
Non-polymers79,635360
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
hetero molecules
x 5


  • icosahedral pentamer
  • 951 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)950,75060
Polymers944,11430
Non-polymers6,63630
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.14 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,140,90072
Polymers1,132,93736
Non-polymers7,96336
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein E protein


Mass: 54444.051 Da / Num. of mol.: 3 / Fragment: UNP residues 291-794 / Source method: isolated from a natural source
Source: (natural) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
References: UniProt: A0A024B7W1
#2: Protein M protein


Mass: 8496.883 Da / Num. of mol.: 3 / Fragment: UNP residues 216-290 / Source method: isolated from a natural source
Source: (natural) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
References: UniProt: A0A024B7W1
#3: Sugar
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Zika virus / Type: VIRUS / Entity ID: 1, 2 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Strain: ZIKV/Human/French Polynesia/10087PF/2013
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 500 nm / Triangulation number (T number): 3
Buffer solutionpH: 8 / Details: 12 mM Tris-HCl, pH 8, 120 mM NaCl, 1 mM EDTA
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 400 divisions/in.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 18000 X / Calibrated magnification: 30864 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 100 K
Image recordingAverage exposure time: 11 sec. / Electron dose: 33.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2085
Image scansSampling size: 5 µm / Width: 7420 / Height: 7676 / Movie frames/image: 55

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2Appion3.2particle selection
3Leginon3.2image acquisition
5CTFFIND4CTF correction
6jsprCTF correction
9Cootmodel fitting
11PHENIXmodel refinement
12jsprinitial Euler assignment
13jsprfinal Euler assignment
14RELION2.1classification
15jspr3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 108963
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35842
Details: Soft mask was applied to the even/odd map before FSC calculation.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: Real space followed by reciprocal space
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813547
ELECTRON MICROSCOPYf_angle_d1.08118369
ELECTRON MICROSCOPYf_dihedral_angle_d8.4497957
ELECTRON MICROSCOPYf_chiral_restr0.0592094
ELECTRON MICROSCOPYf_plane_restr0.0062312

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