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- EMDB-27318: CryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2F... -

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Basic information

Entry
Database: EMDB / ID: EMD-27318
TitleCryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2Fabs ANDV-5 and ANDV-34
Map data
Sample
  • Complex: Gn(H) in complex with Fabs ANDV-5 ANDV-34
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Fv (H) ANDV-34
    • Protein or peptide: Fv (L) ANDV-34
    • Protein or peptide: Fv (H) ANDV-5
    • Protein or peptide: Fv (L) ANDV-5
    • Protein or peptide: COV44-79 heavy chain constant domain
    • Protein or peptide: Fab Fc (L) KappaC
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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / 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 speciesHomo sapiens (human) / Andes orthohantavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27318.png

Downloads & links

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Map

FileDownload / File: emd_27318.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.46 Å
Density
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-31.775303 - 41.340607
Average (Standard dev.)1.1335668e-11 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27318_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27318_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gn(H) in complex with Fabs ANDV-5 ANDV-34

EntireName: Gn(H) in complex with Fabs ANDV-5 ANDV-34
Components
  • Complex: Gn(H) in complex with Fabs ANDV-5 ANDV-34
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Fv (H) ANDV-34
    • Protein or peptide: Fv (L) ANDV-34
    • Protein or peptide: Fv (H) ANDV-5
    • Protein or peptide: Fv (L) ANDV-5
    • Protein or peptide: COV44-79 heavy chain constant domain
    • Protein or peptide: Fab Fc (L) KappaC

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Supramolecule #1: Gn(H) in complex with Fabs ANDV-5 ANDV-34

SupramoleculeName: Gn(H) in complex with Fabs ANDV-5 ANDV-34 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycoprotein N

MacromoleculeName: Glycoprotein N / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Andes orthohantavirus
Molecular weightTheoretical: 38.767207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TIYELKMECP HTVGLGQGYI IGSTELGLIS IEAASDIKLE SSCNFDLHTT SMAQKSFTQV EWRKKSDTTD TTNAASTTFE AQTKTVNLR GTCILAPELY DTLKKVKKTV LCYDLTCNQT HCQPTVYLIA PVLTCMSIRS CMASVFTSRI QVIYEKTHCV T GQLIEGQC ...String:
TIYELKMECP HTVGLGQGYI IGSTELGLIS IEAASDIKLE SSCNFDLHTT SMAQKSFTQV EWRKKSDTTD TTNAASTTFE AQTKTVNLR GTCILAPELY DTLKKVKKTV LCYDLTCNQT HCQPTVYLIA PVLTCMSIRS CMASVFTSRI QVIYEKTHCV T GQLIEGQC FNPAHTLTLS QPAHTYDTVT LPISCFFTPK KSEQLKVIKT FEGILTKTGC TENALQGYYV CFLGSHSEPL IV PSLEDIR SAEVVSRMLV HPRGEDHDAI QNSQSHLRIV GPITAKVPST SSTDTLKGTA FAGVPMYSSL STLVRNADPE FVF SPGIVP ESNHSTCDKK TVPITWTGYL PISGEME

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Macromolecule #2: Fv (H) ANDV-34

MacromoleculeName: Fv (H) ANDV-34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.609076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVHLVQSGGE LRKPGSSVKV SCKASGGTFS SFAITWLRQA PGQGLEWVGA YIPVFGSAIH GQKVHGRVTL TADESTTTAY MELSSLRSE DTAVYFCARG PTQNWEYSYY TYFESWGQGT LVTVSS

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Macromolecule #3: Fv (L) ANDV-34

MacromoleculeName: Fv (L) ANDV-34 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.91224 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIVLTQSPGT LSLSPGERAT LSCRASQSVT SRYLAWYQQK PGQAPRLLIY DTSSRATGIP DRFSGSGSET DFTLTISRLA PEDFAVYYC QQYGTSPAVT FGQGTRLEIK

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Macromolecule #4: Fv (H) ANDV-5

MacromoleculeName: Fv (H) ANDV-5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.013572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLLQSGAE VKKPGSSVRV SCQSSGDIYN YYGISWVRQA PGQGLEWMGG IIPVYGRPNY VQKFRGRVTF TVDKSTSTAY MELSTLRAD DTAVYYCARD TARSHYFGSG NDYGMDVWGQ GTTVIVSS

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Macromolecule #5: Fv (L) ANDV-5

MacromoleculeName: Fv (L) ANDV-5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.187647 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGFNFVDW YLQKPGQSPQ LLIYLGSTRA SGVPDRFSGS GSGTDFTLEI SRVEAEDVG VYYCMQALQF PRTFGQGTKL DIK

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Macromolecule #6: COV44-79 heavy chain constant domain

MacromoleculeName: COV44-79 heavy chain constant domain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.58592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKP SNTKVDKKVE PKSC

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Macromolecule #7: Fab Fc (L) KappaC

MacromoleculeName: Fab Fc (L) KappaC / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.848126 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEV THQGLRSPVT KSFNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3110 / Average exposure time: 4.34 sec. / Average electron dose: 50.86 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 208851
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8dbz:
CryoEM structure of Hantavirus ANDV Gn(H) protein complex with 2Fabs ANDV-5 and ANDV-34

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