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- EMDB-27995: HMPV F dimer bound to RSV-199 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-27995
TitleHMPV F dimer bound to RSV-199 Fab
Map data
Sample
  • Complex: MPV fusion protein complex with RSV-199 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: RSV-199 light chain protein
    • Protein or peptide: RSV-199 heavy chain protein
KeywordsHuman antibody / RSV and MPV fusion protein / complex cryo-EM structure / Biosynthetic protein / viral protein and antiviral protein
Biological speciesHuman metapneumovirus / Human metapneumovirus A / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.38 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)R01A137523 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 31, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27995.png

Downloads & links

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Map

FileDownload / File: emd_27995.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.351
Minimum - Maximum-1.1651027 - 2.5237226
Average (Standard dev.)0.0050007636 (±0.06166879)
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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Additional map: #1

Fileemd_27995_additional_1.map
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Half map: #2

Fileemd_27995_half_map_1.map
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Half map: #1

Fileemd_27995_half_map_2.map
Projections & Slices
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Sample components

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Entire : MPV fusion protein complex with RSV-199 Fab

EntireName: MPV fusion protein complex with RSV-199 Fab
Components
  • Complex: MPV fusion protein complex with RSV-199 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: RSV-199 light chain protein
    • Protein or peptide: RSV-199 heavy chain protein

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Supramolecule #1: MPV fusion protein complex with RSV-199 Fab

SupramoleculeName: MPV fusion protein complex with RSV-199 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus A
Molecular weightTheoretical: 47.513301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RRRRFVLGA IALGVCTAAA VTAGVAIAKT IRLESEVTAI KNALKKTNEA VSTLGNGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD ...String:
LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RRRRFVLGA 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 VYQLSKVEGE QHVIKGRPVS SSFDPVKFPE

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Macromolecule #2: RSV-199 light chain protein

MacromoleculeName: RSV-199 light chain protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.819264 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAVVTQPPSV SGAPGQRVII SCTGSGSNLG ADYGVHWYQQ LPGTAPKLLI YGDRNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRSLNW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV N AGVETTKP ...String:
QAVVTQPPSV SGAPGQRVII SCTGSGSNLG ADYGVHWYQQ LPGTAPKLLI YGDRNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRSLNW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV N AGVETTKP SKQSNNKYAA SSYLSLTPEQ WKSHKSYSCQ VTHEGSTVEK TVAPAECS

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Macromolecule #3: RSV-199 heavy chain protein

MacromoleculeName: RSV-199 heavy chain protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.022906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVKPGGSLRV SCVVSGFTFS SYRMHWVRQA PGKGLEWVSS ITASSSYINY AESVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD ENTGISHYWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLVESGGG VVKPGGSLRV SCVVSGFTFS SYRMHWVRQA PGKGLEWVSS ITASSSYINY AESVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD ENTGISHYWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 40.0 µm / Nominal defocus min: 3.451 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 563257
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 100

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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-8ebp:
HMPV F dimer bound to RSV-199 Fab

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