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- PDB-6mid: Cryo-EM structure of the ZIKV virion in complex with Fab fragment... -

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Entry
Database: PDB / ID: 6mid
TitleCryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Components
  • E protein
  • M protein
  • monoclonal antibody ZIKV-195 heavy chain
  • monoclonal antibody ZIKV-195 light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / monoclonal antibody / complex / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


flavivirin / immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding ...flavivirin / immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / centrosome / lipid binding / viral envelope / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular space / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane
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 / Monooxygenase ...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 / Monooxygenase / : / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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 envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Helicase, Ruva Protein; domain 3 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / Immunoglobulin-like fold / 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
Genome polyprotein / Immunoglobulin lambda variable 1-36
Similarity search - Component
Biological speciesZika virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLong, F. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI076331 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope.
Authors: Feng Long / Michael Doyle / Estefania Fernandez / Andrew S Miller / Thomas Klose / Madhumati Sevvana / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Richard J Kuhn / Michael S Diamond ...Authors: Feng Long / Michael Doyle / Estefania Fernandez / Andrew S Miller / Thomas Klose / Madhumati Sevvana / Aubrey Bryan / Edgar Davidson / Benjamin J Doranz / Richard J Kuhn / Michael S Diamond / James E Crowe / Michael G Rossmann /
Abstract: Zika virus (ZIKV) is a major human pathogen and member of the genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and ...Zika virus (ZIKV) is a major human pathogen and member of the genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and from mother to fetus in humans. During recent outbreaks, ZIKV infections have been linked to microcephaly, congenital disease, and Guillain-Barré syndrome. Neutralizing antibodies have potential as therapeutic agents. We report here a 4-Å-resolution cryo-electron microscopy structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. The footprint of the ZIKV-195 Fab fragment expands across two adjacent envelope (E) protein protomers. ZIKV neutralization by this antibody is presumably accomplished by cross-linking the E proteins, which likely prevents formation of E protein trimers required for fusion of the viral and cellular membranes. A single dose of ZIKV-195 administered 5 days after virus inoculation showed marked protection against lethality in a stringent mouse model of infection.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 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

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  • 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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Assembly

Deposited unit
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,99611
Polymers214,7228
Non-polymers1,2733
Water00
1
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)12,959,739660
Polymers12,883,347480
Non-polymers76,392180
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: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 5


  • icosahedral pentamer
  • 1.08 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,079,97855
Polymers1,073,61240
Non-polymers6,36615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E protein
B: M protein
C: E protein
D: M protein
E: E protein
F: M protein
H: monoclonal antibody ZIKV-195 heavy chain
L: monoclonal antibody ZIKV-195 light chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.3 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,295,97466
Polymers1,288,33548
Non-polymers7,63918
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 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 (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/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 (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Strain: isolate ZIKV/Human/French Polynesia/10087PF/2013 / References: UniProt: A0A024B7W1
#3: Antibody monoclonal antibody ZIKV-195 heavy chain


Mass: 14148.739 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Antibody monoclonal antibody ZIKV-195 light chain


Mass: 11750.902 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A0B4J1U3
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195COMPLEXPurified from infected Vero cells overexpressing the furin protease#1-#40MULTIPLE SOURCES
2Zika virusVIRUS#1-#21NATURAL
3monoclonal antibody ZIKV-195COMPLEX#3-#41NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)2043570isolate ZIKV/Human/French Polynesia/10087PF/2013
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8 / Details: NTE buffer at pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2120 mMsodium chlorideNaCl1
31 mMEDTA1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Fab fragments were mixed with purified mature virus particles to make complexes.
Specimen supportDetails: unspecified
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K

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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
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1691

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Processing

EM software
IDNameVersionCategoryDetails
1FindEMparticle selection
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
8EMfitmodel fitting
10jsprinitial Euler assignment
11jsprfinal Euler assignment
12RELIONclassification
13jspr3D reconstruction
20PHENIXmodel refinementreal space refinement
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10687
Details: The map was masked by removing the internal nucleic acid region and the external background region.
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: The occupancy of bound Fabs was low. Due to poor density, only the variable domain of Fab molecule was modeled and fit into one of the three Fab binding sites on each icosahedral asymmetric unit.
Atomic model buildingPDB-ID: 6CO8

6co8


Accession code: 6CO8 / Source name: PDB / Type: experimental model

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