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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 / homologyFlavivirus 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 2.1.1.56 and EC 2.1.1.57) 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 / RNA helicase / 4 iron, 4 sulfur cluster binding / nucleoside-triphosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / fusion of virus membrane with host endosome membrane / 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
Specimen sourceZika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsSevvana, M. / Long, F. / Miller, A.J. / Klose, T. / Buda, G. / Sun, L. / Kuhn, R.J. / Rossmann, M.R.
CitationJournal: 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
DateDeposition: Mar 12, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 11, 2018Structure modelData collection / Database references / Source and taxonomycitation / citation_author / em_entity_assembly_naturalsource / entity_src_nat_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

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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
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  • Superimposition on EM map
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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
Polyers188,8236
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
Polyers11,329,368360
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
Polyers944,11430
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
Polyers1,132,93736
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

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Components

#1: Protein/peptide E protein


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


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


Mass: 221.208 Da / Num. of mol.: 6 / Formula: C8H15NO6 / N-Acetylglucosamine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellDiameter: 500 nm / Triangulation number (T number): 3
Buffer solutionDetails: 12 mM Tris-HCl, pH 8, 120 mM NaCl, 1 mM EDTA / pH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 400
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / Calibrated magnification: 30864 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 100 kelvins
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) / Number of grids imaged: 1 / Number of real images: 2085
Image scansSampling size: 5 microns / 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 selectionNumber of particles selected: 108963
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 35842
Details: Soft mask was applied to the even/odd map before FSC calculation.
Symmetry type: POINT
Atomic model buildingDetails: Real space followed by reciprocal space / Ref protocol: RIGID BODY FIT / Ref space: REAL
Refine LS restraints
Refine 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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