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- PDB-5iz7: Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 -

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Basic information

Entry
Database: PDB / ID: 5iz7
TitleCryo-EM structure of thermally stable Zika virus strain H/PF/2013
Components
  • structural protein E
  • structural protein M
KeywordsVIRUS / viral protein / flavivirus / glycoprotein / zika virus
Function / homology
Function and homology information


response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid ...response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus envelope glycoprotein M-like / Monooxygenase - #260 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Photosystem II protein D1 ...Flavivirus envelope glycoprotein M-like / Monooxygenase - #260 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Photosystem II protein D1 / Monooxygenase / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / : / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Helicase, Ruva Protein; domain 3 / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Photosystem q(B) protein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKostyuchenko, V.A. / Zhang, S. / Fibriansah, G. / Lok, S.M.
Funding support Singapore, 3items
OrganizationGrant numberCountry
Ministry of EducationMOE2012-T3-1-008 Singapore
National Research FoundationNRF-NRFI2016-01 Singapore
Ministry of HealthDuke-NUS Signature Research Program Singapore
CitationJournal: Nature / Year: 2016
Title: Structure of the thermally stable Zika virus.
Authors: Victor A Kostyuchenko / Elisa X Y Lim / Shuijun Zhang / Guntur Fibriansah / Thiam-Seng Ng / Justin S G Ooi / Jian Shi / Shee-Mei Lok /
Abstract: Zika virus (ZIKV), formerly a neglected pathogen, has recently been associated with microcephaly in fetuses, and with Guillian-Barré syndrome in adults. Here we present the 3.7 Å resolution cryo- ...Zika virus (ZIKV), formerly a neglected pathogen, has recently been associated with microcephaly in fetuses, and with Guillian-Barré syndrome in adults. Here we present the 3.7 Å resolution cryo-electron microscopy structure of ZIKV, and show that the overall architecture of the virus is similar to that of other flaviviruses. Sequence and structural comparisons of the ZIKV envelope (E) protein with other flaviviruses show that parts of the E protein closely resemble the neurovirulent West Nile and Japanese encephalitis viruses, while others are similar to dengue virus (DENV). However, the contribution of the E protein to flavivirus pathobiology is currently not understood. The virus particle was observed to be structurally stable even when incubated at 40 °C, in sharp contrast to the less thermally stable DENV. This is also reflected in the infectivity of ZIKV compared to DENV serotypes 2 and 4 (DENV2 and DENV4) at different temperatures. The cryo-electron microscopy structure shows a virus with a more compact surface. This structural stability of the virus may help it to survive in the harsh conditions of semen, saliva and urine. Antibodies or drugs that destabilize the structure may help to reduce the disease outcome or limit the spread of the virus.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Other
Category: atom_sites / cell ...atom_sites / cell / citation / em_software
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c / _citation.journal_id_CSD / _em_software.name
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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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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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,4869
Polymers188,8236
Non-polymers6643
Water00
1
A: structural protein E
C: structural protein E
D: structural protein M
B: structural protein E
E: structural protein M
F: structural protein M
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)11,369,186540
Polymers11,329,368360
Non-polymers39,817180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: structural protein E
C: structural protein E
D: structural protein M
B: structural protein E
E: structural protein M
F: structural protein M
hetero molecules
x 5


  • icosahedral pentamer
  • 947 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)947,43245
Polymers944,11430
Non-polymers3,31815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: structural protein E
C: structural protein E
D: structural protein M
B: structural protein E
E: structural protein M
F: structural protein M
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.14 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,136,91954
Polymers1,132,93736
Non-polymers3,98218
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 structural protein E


Mass: 54444.051 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: glycosylated at N154 / Source: (natural) Zika virus / Cell line: C6/36 / Strain: H/PF/2013 / References: UniProt: A0A024B7W1
#2: Protein structural protein M


Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / Cell line: C6/36 / Strain: H/PF/2013 / References: UniProt: A0A0U4DG08, UniProt: A0A024B7W1*PLUS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY

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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 weightValue: 10 MDa / Experimental value: NO
Source (natural)Organism: Zika virus / Strain: H/PF/2013
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: glycoprotein shell / Diameter: 480 nm / Triangulation number (T number): 1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris-HClC4H12ClNO31
2120 mMSodium ChlorideNaCl1
31 mMEDTAC10H16N2O81
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: purified with PEG precipitation, sucrose cushion and potassium tartrate gradient
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: blot for 1s

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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 FIELD / Cs: 2.7 mm
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 50 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3086
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 30 / Used frames/image: 2-11

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selection
4ctffind417CTF correction
7Coot0.8.3model fitting
9EMAN1.9initial Euler assignmentMPSA
10EMAN1.9final Euler assignmentMPSA
12EMAN1.93D reconstruction
13CNS1.3model refinementelectron scattering factors used
Image processingDetails: images collected in movie mode, 30 frames per 1.8s exposure; frames aligned with MotionCorr, frames 2-11 averaged to produce images for further processing
CTF correctionDetails: correction for astigmatism included / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 11600 / Details: manually picked
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7180 / Algorithm: FOURIER SPACE / Num. of class averages: 7180 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: RECIPROCAL / Target criteria: residual
Details: Only icosahedral symmetry imposed. Rwork 0.323 Rtest 0.324
Atomic model building

3D fitting-ID: 1 / Accession code: 3J27 / Initial refinement model-ID: 1 / PDB-ID: 3J27

3j27

/ Source name: PDB / Type: experimental model

IDPdb chain-IDPdb chain residue range
1A1-495
2B1-72

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