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- PDB-7cbp: CryoEM structure of Zika virus with Fab at 4.1 Angstrom -

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Basic information

Entry
Database: PDB / ID: 7cbp
TitleCryoEM structure of Zika virus with Fab at 4.1 Angstrom
Components
  • Envelope protein E
  • Fab Heavy chain
  • Fab light chain
  • Small envelope protein M
KeywordsVIRUS / Zika virus / Fab antibody
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 / metal ion binding
Similarity search - Function
Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Flavivirus envelope glycoprotein M / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein, central and dimerisation domains
Similarity search - Domain/homology
Photosystem q(B) protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Zika virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsTyagi, A. / Ahmed, T. / Shi, J. / Bhushan, S.
Funding support1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)2017-T1- 001-022 (RG34/17), MOE2017-T2-2-089
CitationJournal: J Struct Biol X / Year: 2020
Title: A complex between the Zika virion and the Fab of a broadly cross-reactive neutralizing monoclonal antibody revealed by cryo-EM and single particle analysis at 4.1 Å resolution.
Authors: Anu Tyagi / Tofayel Ahmed / Jian Shi / Shashi Bhushan /
Abstract: Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class ...Zika virus (ZIKV) recently emerged as a major public health concern because it can cause fetal microcephaly and neurological disease such as the Guillain-Barré syndrome. A particularly potent class of broadly neutralizing antibodies (nAbs) targets a quaternary epitope located at the interface of two envelope proteins monomers, exposed at the surface of the mature virion. This "E-dimer-dependent epitope" (EDE), comprises the fusion loop of one monomer at the tip of domain II of E and a portion of the domains I and III of the adjacent monomer. Since this epitope largely overlaps with the binding site of the precursor membrane protein (prM) during Zika virion maturation, its molecular surface is evolutionary conserved in flaviviruses such as Dengue and Zika viruses, and can elicit antibodies that broadly neutralize various ZIKV strains. Here, we present a cryo-EM reconstruction at 4.1 Å resolution of the virion bound to the antigen binding fragment (Fab) of an antibody that targets this mutationally-constrained quaternary epitope. The Fab incompletely covers the surface of the virion as it does not bind next to its 5-fold icosahedral axes. The structure reveals details of the binding mode of this potent neutralizing class of antibodies and can inform the design of immunogens and vaccines targeting this conserved epitope.
History
DepositionJun 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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 / pdbx_validate_close_contact / 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 / _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_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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

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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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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
T: Small envelope protein M
U: Small envelope protein M
V: Small envelope protein M
Q: Envelope protein E
N: Envelope protein E
K: Envelope protein E
D: Fab Heavy chain
E: Fab light chain
R: Fab Heavy chain
S: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,33711
Polymers282,91310
Non-polymers4241
Water00
1
T: Small envelope protein M
U: Small envelope protein M
V: Small envelope protein M
Q: Envelope protein E
N: Envelope protein E
K: Envelope protein E
D: Fab Heavy chain
E: Fab light chain
R: Fab Heavy chain
S: Fab light chain
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)17,000,224660
Polymers16,974,760600
Non-polymers25,46460
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
T: Small envelope protein M
U: Small envelope protein M
V: Small envelope protein M
Q: Envelope protein E
N: Envelope protein E
K: Envelope protein E
D: Fab Heavy chain
E: Fab light chain
R: Fab Heavy chain
S: Fab light chain
hetero molecules
x 5


  • icosahedral pentamer
  • 1.42 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,416,68555
Polymers1,414,56350
Non-polymers2,1225
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
T: Small envelope protein M
U: Small envelope protein M
V: Small envelope protein M
Q: Envelope protein E
N: Envelope protein E
K: Envelope protein E
D: Fab Heavy chain
E: Fab light chain
R: Fab Heavy chain
S: Fab light chain
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.7 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,700,02266
Polymers1,697,47660
Non-polymers2,5466
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 Small envelope protein M / 64320


Mass: 8496.883 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / References: UniProt: A0A024B7W1
#2: Protein Envelope protein E


Mass: 54186.762 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Zika virus / References: UniProt: A0A024B7W1
#3: Antibody Fab Heavy chain


Mass: 23612.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab light chain


Mass: 23818.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 424.401 Da / Num. of mol.: 1
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 ligand of interestN

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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
IDNameTypeEntity IDParent-IDSource
1Zika virusCOMPLEX#1-#40MULTIPLE SOURCES
2Zika virus M and E proteinsCOMPLEX#1-#21NATURAL
3FABCOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Zika virus64320
23Homo sapiens (human)9606
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: RELION / Category: classification
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4610 / Symmetry type: POINT

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