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- PDB-5ire: The cryo-EM structure of Zika Virus -

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Basic information

Entry
Database: PDB / ID: 5ire
TitleThe cryo-EM structure of Zika Virus
Components
  • E protein
  • M protein
KeywordsVIRUS / Zika virus
Function / homologyHelicase, C-terminal / Flavivirus non-structural protein NS2A / 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 / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus ...Helicase, C-terminal / Flavivirus non-structural protein NS2A / 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 / 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 NS2B / Flavivirus capsid protein C / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Genome polyprotein, Flavivirus / 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 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Helicase superfamily 1/2, ATP-binding domain / Envelope glycoprotein M superfamily, flavivirus / 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 NS4A / Flavivirus non-structural protein NS4B / 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 / Flaviviral glycoprotein E, central domain, subdomain 2 / suppression by virus of host TYK2 activity / flavivirin / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / suppression by virus of host STAT1 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ATP-dependent helicase activity / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase activity / 4 iron, 4 sulfur cluster binding / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / 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 / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein / E protein / Genome polyprotein
Function and homology information
Specimen sourceZika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsSirohi, D. / Chen, Z. / Sun, L. / Klose, T. / Pierson, T. / Rossmann, M. / Kuhn, 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 13, 2016 / Release: Mar 30, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 30, 2016Structure modelrepositoryInitial release
1.1Apr 6, 2016Structure modelOther
1.2May 4, 2016Structure modelDerived calculations
1.3Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.4Jul 18, 2018Structure modelData collectionem_software_em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-8116
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  • Superimposition on EM map
  • EMDB-8116
  • Imaged by UCSF Chimera
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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 / capsid E protein


Mass: 54444.051 Da / Num. of mol.: 3 / Source: (natural) Zika virus / References: UniProt: A0A060H177, UniProt: A0A024B7W1*PLUS
#2: Protein/peptide M protein


Mass: 8496.883 Da / Num. of mol.: 3 / Fragment: UNP residues 179-253 / Source: (natural) Zika virus / References: UniProt: A0A096XFQ2, UniProt: A0A024B7W1*PLUS
#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
Details: Low passage Vero cells, derived from African green monkey kidney cells, were chosen for propagating the virus.
Entity ID: 1,2,3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Zika virus
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid shell / Diameter: 490 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
1100 mMsodium chlorideNacl1
220 MMTrisTris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: UC-A on holey carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 298 kelvins
Details: Blot for 5 seconds before plunging into liquid ethane (GATAN CRYOPLUNGE 3).

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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: 14000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 kelvins / Temperature (min): 80 kelvins
Image recordingAverage exposure time: 14 sec. / Electron dose: 23 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: 2974
Image scansSampling size: 1.04 microns / Width: 7420 / Height: 7676 / Movie frames/image: 70 / Used frames/image: 2-70

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Processing

EM software
IDNameVersionCategory
1Appion3.2particle selection
2Leginonimage acquisition
4CTFFIND3CTF correction
9PHENIX1.10.1-2155model refinement
10jspr2015initial Euler assignment
11jspr2015final Euler assignment
12jspr2015classification
13jspr20153D reconstruction
Image processingDetails: The images were normalized.
CTF correctionDetails: Phase flipping was performed during 3D reconstruction.
Type: PHASE FLIPPING ONLY
Particle selectionDetails: Particles were picked from 2-binned images using the template-picking method from Appion.
Number of particles selected: 64518
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 11842 / Algorithm: FOURIER SPACE
Details: Soft mark was applied to the even/odd map before FSC calculation.
Number of class averages: 3 / Symmetry type: POINT
Atomic model buildingOverall b value: 150 / Ref protocol: AB INITIO MODEL / Ref space: REAL
Target criteria: T = Tmap + weight * TrestraintsT = Tmap + weight * Trestraints

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