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- EMDB-27990: HMPV F complex with 4I3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-27990
TitleHMPV F complex with 4I3 Fab
Map data
Sample
  • Complex: MPV fusion protein complex with 4I3 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 4I3 heavy chain protein
    • Protein or peptide: 4I3 light chain protein
Keywordshuman antibodies / RSV and MPV Fusion protein / complex Cryo-EM structure / viral protein and antiviral protein / BIOSYNTHETIC PROTEIN
Biological speciesHuman metapneumovirus / Human metapneumovirus A / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.33 Å
AuthorsWen X / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI137523 United States
CitationJournal: Cell Host Microbe / Year: 2023
Title: Potent cross-neutralization of respiratory syncytial virus and human metapneumovirus through a structurally conserved antibody recognition mode.
Authors: Xiaolin Wen / Naveenchandra Suryadevara / Nurgun Kose / Jing Liu / Xiaoyan Zhan / Laura S Handal / Lauren E Williamson / Andrew Trivette / Robert H Carnahan / Theodore S Jardetzky / James E Crowe /
Abstract: Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F ...Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F antibodies from a human donor. One antibody (RSV-199) potently cross-neutralized 8 RSV and hMPV strains by recognizing antigenic site III, which is partially conserved in RSV and hMPV F. Next, we determined the cryoelectron microscopy (cryo-EM) structures of RSV-199 bound to RSV F trimers, hMPV F monomers, and an unexpected dimeric form of hMPV F. These structures revealed how RSV-199 engages both RSV and hMPV F proteins through conserved interactions of the antibody heavy-chain variable region and how variability within heavy-chain complementarity-determining region 3 (HCDR3) can be accommodated at the F protein interface in site-III-directed antibodies. Furthermore, RSV-199 offered enhanced protection against RSV A and B strains and hMPV in cotton rats. These findings highlight the mechanisms of broad neutralization and therapeutic potential of RSV-199.
History
DepositionAug 30, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27990.png

Downloads & links

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Map

FileDownload / File: emd_27990.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.496
Minimum - Maximum-4.97388 - 8.235033
Average (Standard dev.)-0.00087320374 (±0.10104622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 284.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27990_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_27990_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MPV fusion protein complex with 4I3 Fab

EntireName: MPV fusion protein complex with 4I3 Fab
Components
  • Complex: MPV fusion protein complex with 4I3 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 4I3 heavy chain protein
    • Protein or peptide: 4I3 light chain protein

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Supramolecule #1: MPV fusion protein complex with 4I3 Fab

SupramoleculeName: MPV fusion protein complex with 4I3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human metapneumovirus

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus A
Molecular weightTheoretical: 45.044461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RQSRFVLGA IALGVCTAAA VTAGVAIAKT IRLESEVTAI KNALKKTNEA VSTLGNGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD ...String:
LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RQSRFVLGA IALGVCTAAA VTAGVAIAKT IRLESEVTAI KNALKKTNEA VSTLGNGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSNMPT SAGQIKLMLE NRAMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI VKAAPSCSEK KGNYACLLRE DQGWYCQNAG STVYYPNEKD CETRGDHVFC DTA CGINVA EQSKECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLN KGCSYITNQD ADTV TIDNT VYQLSKVEG

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Macromolecule #2: 4I3 heavy chain protein

MacromoleculeName: 4I3 heavy chain protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.376045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIS NYYWNWIRQP PGKGLEWIGY FYYSGSTKYN PSLKSRVTIS LDMSKNQFSL KLRSVTAAD TAVYYCARGT MRESGMPDAF DIWGQGTVVT VS

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Macromolecule #3: 4I3 light chain protein

MacromoleculeName: 4I3 light chain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.438607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELIQPPSV SVSPGQTAII TCSGNNLGNK YACWYQQKAG QSPVMIIYQD NRRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSSVVFGGG TKLTVLGQ

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 36.522 µm / Nominal defocus min: 11.445 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2774162
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4dag

Initial angle assignmentType: OTHER
Final 3D classificationNumber classes: 100 / Software - Name: cryoSPARC
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 226482

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Atomic model buiding 1

Initial modelPDB ID:

4dag


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8eay:
HMPV F complex with 4I3 Fab

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