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- PDB-7tqu: Coxsackievirus A21 capsid subdomain in complex with mouse polyclo... -

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Basic information

Entry
Database: PDB / ID: 7tqu
TitleCoxsackievirus A21 capsid subdomain in complex with mouse polyclonal antibody pAbC-1
Components
  • VP1
  • VP2
  • VP3
  • VP4
  • pAbC-1 heavy chain
  • pAbC-1 light chain
KeywordsVIRUS/IMMUNE SYSTEM / polyclonal antibodies / immune complex / cryoEM / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell ...: / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MYRISTIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Coxsackievirus A21
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAntanasijevic, A. / Ward, A.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: PNAS Nexus / Year: 2022
Title: High-resolution structural analysis of enterovirus-reactive polyclonal antibodies in complex with whole virions.
Authors: Aleksandar Antanasijevic / Autumn J Schulze / Vijay S Reddy / Andrew B Ward /
Abstract: Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 ...Non-polio enteroviruses (NPEVs) cause serious illnesses in young children and neonates, including aseptic meningitis, encephalitis, and inflammatory muscle disease, among others. While over 100 serotypes have been described to date, vaccine only exists for EV-A71. Efforts toward rationally designed pan-NPEV vaccines would greatly benefit from structural biology methods for rapid and comprehensive evaluation of vaccine candidates and elicited antibody responses. Toward this goal, we introduced a cryo-electron-microscopy-based approach for structural analysis of virus- or vaccine-elicited polyclonal antibodies (pAbs) in complex with whole NPEV virions. We demonstrated the feasibility using coxsackievirus A21 and reconstructed five structurally distinct pAbs bound to the virus. The pAbs targeted two immunodominant epitopes, one overlapping with the receptor binding site. These results demonstrate that our method can be applied to map broad-spectrum polyclonal immune responses against intact virions and define potentially cross-reactive epitopes.
History
DepositionJan 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: pAbC-1 heavy chain
L: pAbC-1 light chain
a: VP1
b: VP2
c: VP3
d: VP4
e: VP1
f: VP2
g: VP3
h: VP4
i: VP1
j: VP2
k: VP3
l: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,50817
Polymers309,82314
Non-polymers6853
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 14 molecules HLaeibfjcgkdhl

#1: Protein pAbC-1 heavy chain


Mass: 9549.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Heavy Chain of the polyclonal antibody pAbC-1 / Source: (natural) Mus musculus (house mouse)
#2: Protein pAbC-1 light chain


Mass: 8698.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Light Chain of the polyclonal antibody pAbC-1 / Source: (natural) Mus musculus (house mouse)
#3: Protein VP1


Mass: 33234.238 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VP1 protein of the coxsackievirus A21 capsid / Source: (natural) Coxsackievirus A21
References: UniProt: Q7T7N6, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein VP2


Mass: 29918.537 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VP2 protein of the coxsackievirus A21 capsid / Source: (natural) Coxsackievirus A21
References: UniProt: Q7T7N6, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#5: Protein VP3


Mass: 26596.703 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VP3 protein of the coxsackievirus A21 capsid / Source: (natural) Coxsackievirus A21
References: UniProt: Q7T7N6, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#6: Protein VP4


Mass: 7442.118 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: VP4 protein of the coxsackievirus A21 capsid / Source: (natural) Coxsackievirus A21
References: UniProt: Q7T7N6, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Non-polymers , 1 types, 3 molecules

#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2

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Details

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

ComponentName: Immune complex featuring subdomains of coxsackievirus A21 (CV-A21) viral particles in complex with mouse polyclonal antibodies
Type: COMPLEX
Details: The complexes were assembled by combining purified CV-A21 particles and polyclonal antibodies isolated from mice (as Fab fragments)
Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Coxsackievirus A2112069
31Mus musculus (house mouse)10090
Buffer solutionpH: 7.4 / Details: TBS, 0.2um filtered
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris-HClTrisTris-HClTris1
2150 mMSodium chlorideNaClSodium chloride1
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The complex was generated by incubation of mouse polyclonal antibodies with recombinantly expressed CV-A21 virions and subsequent SEC purification.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 10 % / Chamber temperature: 283 K / Details: 3-7s blot time

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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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3862
Image scansSampling size: 5 µm / Movie frames/image: 45

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RosettaEMmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
Image processingDetails: MotionCor2 was used for frame alignment
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 22937
Details: Cryosparc template picker. Following the 2D classification and symmetry expansion the number of particles was 1334700. Symmetry-expanded particles were used for 3D classification and refinement.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19748 / Algorithm: BACK PROJECTION / Details: 19748 symmetry-expanded particles / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 1Z7S

1z7s

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