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- PDB-8dbz: CryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2F... -

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Basic information

Entry
Database: PDB / ID: 8dbz
TitleCryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2Fabs ANDV-5 and ANDV-34
Components
  • COV44-79 heavy chain constant domain
  • Fab Fc (L) KappaC
  • Fv (H) ANDV-34
  • Fv (H) ANDV-5
  • Fv (L) ANDV-34
  • Fv (L) ANDV-5
  • Glycoprotein N
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / immunoglobulin complex / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / adaptive immune response / host cell endoplasmic reticulum membrane / induction by virus of host autophagy ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / immunoglobulin complex / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endocytosis involved in viral entry into host cell / host cell surface / adaptive immune response / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / signal transduction / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Envelopment polyprotein
Similarity search - Component
Biological speciesAndes orthohantavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBinshtein, E. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Advanced Research Projects AgencyP3 HR0011-18-2-0001 United States
CitationJournal: Elife / Year: 2023
Title: Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies.
Authors: Taylor B Engdahl / Elad Binshtein / Rebecca L Brocato / Natalia A Kuzmina / Lucia M Principe / Steven A Kwilas / Robert K Kim / Nathaniel S Chapman / Monique S Porter / Pablo Guardado-Calvo ...Authors: Taylor B Engdahl / Elad Binshtein / Rebecca L Brocato / Natalia A Kuzmina / Lucia M Principe / Steven A Kwilas / Robert K Kim / Nathaniel S Chapman / Monique S Porter / Pablo Guardado-Calvo / Félix A Rey / Laura S Handal / Summer M Diaz / Irene A Zagol-Ikapitte / Minh H Tran / W Hayes McDonald / Jens Meiler / Joseph X Reidy / Andrew Trivette / Alexander Bukreyev / Jay W Hooper / James E Crowe /
Abstract: Hantaviruses are high-priority emerging pathogens carried by rodents and transmitted to humans by aerosolized excreta or, in rare cases, person-to-person contact. While infections in humans are ...Hantaviruses are high-priority emerging pathogens carried by rodents and transmitted to humans by aerosolized excreta or, in rare cases, person-to-person contact. While infections in humans are relatively rare, mortality rates range from 1 to 40% depending on the hantavirus species. There are currently no FDA-approved vaccines or therapeutics for hantaviruses, and the only treatment for infection is supportive care for respiratory or kidney failure. Additionally, the human humoral immune response to hantavirus infection is incompletely understood, especially the location of major antigenic sites on the viral glycoproteins and conserved neutralizing epitopes. Here, we report antigenic mapping and functional characterization for four neutralizing hantavirus antibodies. The broadly neutralizing antibody SNV-53 targets an interface between Gn/Gc, neutralizes through fusion inhibition and cross-protects against the Old World hantavirus species Hantaan virus when administered pre- or post-exposure. Another broad antibody, SNV-24, also neutralizes through fusion inhibition but targets domain I of Gc and demonstrates weak neutralizing activity to authentic hantaviruses. ANDV-specific, neutralizing antibodies (ANDV-5 and ANDV-34) neutralize through attachment blocking and protect against hantavirus cardiopulmonary syndrome (HCPS) in animals but target two different antigenic faces on the head domain of Gn. Determining the antigenic sites for neutralizing antibodies will contribute to further therapeutic development for hantavirus-related diseases and inform the design of new broadly protective hantavirus vaccines.
History
DepositionJun 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein N
D: Fv (H) ANDV-34
E: Fv (L) ANDV-34
B: Fv (H) ANDV-5
C: Fv (L) ANDV-5
F: COV44-79 heavy chain constant domain
G: Fab Fc (L) KappaC
H: COV44-79 heavy chain constant domain
I: Fab Fc (L) KappaC


Theoretical massNumber of molelcules
Total (without water)135,3589
Polymers135,3589
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 3 molecules AFH

#1: Protein Glycoprotein N / Gn / Glycoprotein G1


Mass: 38767.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Andes orthohantavirus / Gene: GP, ADT63_77597gpM, ADT63_77598gpM / Production host: Homo sapiens (human) / References: UniProt: Q9E006
#6: Protein COV44-79 heavy chain constant domain / Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 10585.920 Da / Num. of mol.: 2 / Fragment: UNP residues 120-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5

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Antibody , 5 types, 6 molecules DEBCGI

#2: Antibody Fv (H) ANDV-34


Mass: 13609.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fv (L) ANDV-34


Mass: 11912.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fv (H) ANDV-5


Mass: 14013.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Fv (L) ANDV-5


Mass: 12187.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#7: Antibody Fab Fc (L) KappaC


Mass: 11848.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: Gn(H) in complex with Fabs ANDV-5 ANDV-34 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.34 sec. / Electron dose: 50.86 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3110

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208851 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038087
ELECTRON MICROSCOPYf_angle_d0.66311050
ELECTRON MICROSCOPYf_dihedral_angle_d5.641248
ELECTRON MICROSCOPYf_chiral_restr0.0461322
ELECTRON MICROSCOPYf_plane_restr0.0051455

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