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- EMDB-43827: Fab 77-stabilized MeV F ectodomain fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-43827
TitleFab 77-stabilized MeV F ectodomain fragment
Map datalocal filtered map
Sample
  • Complex: Fab 77-stabilized MeV F ectodomain fragment
    • Complex: Antibody 77 Fab Heavy Chain, Antibody 77 Fab Light Chain
      • Protein or peptide: mAb 77 light chain
      • Protein or peptide: mAB 77 heavy chain
    • Complex: Measles virus Fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN / glycoprotein / immune system / antibody / measles / high-resolution / antibody fragment / fab / neutralizing antibody / ectodomain
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMus musculus (house mouse) / Measles virus strain Ichinose-B95a / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZyla D / Saphire EO
Funding support Switzerland, United States, 5 items
OrganizationGrant numberCountry
Swiss National Science FoundationP2EZP3_195680 Switzerland
Swiss National Science FoundationP500PB_210992 Switzerland
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS105699 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS091263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI176833 United States
CitationJournal: Science / Year: 2024
Title: A neutralizing antibody prevents postfusion transition of measles virus fusion protein.
Authors: Dawid S Zyla / Roberta Della Marca / Gele Niemeyer / Gillian Zipursky / Kyle Stearns / Cameron Leedale / Elizabeth B Sobolik / Heather M Callaway / Chitra Hariharan / Weiwei Peng / Diptiben ...Authors: Dawid S Zyla / Roberta Della Marca / Gele Niemeyer / Gillian Zipursky / Kyle Stearns / Cameron Leedale / Elizabeth B Sobolik / Heather M Callaway / Chitra Hariharan / Weiwei Peng / Diptiben Parekh / Tara C Marcink / Ruben Diaz Avalos / Branka Horvat / Cyrille Mathieu / Joost Snijder / Alexander L Greninger / Kathryn M Hastie / Stefan Niewiesk / Anne Moscona / Matteo Porotto / Erica Ollmann Saphire /
Abstract: Measles virus (MeV) presents a public health threat that is escalating as vaccine coverage in the general population declines and as populations of immunocompromised individuals, who cannot be ...Measles virus (MeV) presents a public health threat that is escalating as vaccine coverage in the general population declines and as populations of immunocompromised individuals, who cannot be vaccinated, increase. There are no approved therapeutics for MeV. Neutralizing antibodies targeting viral fusion are one potential therapeutic approach but have not yet been structurally characterized or advanced to clinical use. We present cryo-electron microscopy (cryo-EM) structures of prefusion F alone [2.1-angstrom (Å) resolution], F complexed with a fusion-inhibitory peptide (2.3-Å resolution), F complexed with the neutralizing and protective monoclonal antibody (mAb) 77 (2.6-Å resolution), and an additional structure of postfusion F (2.7-Å resolution). In vitro assays and examination of additional EM classes show that mAb 77 binds prefusion F, arrests F in an intermediate state, and prevents transition to the postfusion conformation. These structures shed light on antibody-mediated neutralization that involves arrest of fusion proteins in an intermediate state.
History
DepositionFeb 26, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43827.png

Downloads & links

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Map

FileDownload / File: emd_43827.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 160 pix.
= 224.48 Å		1.4 Å/pix.
x 160 pix.
= 224.48 Å		1.4 Å/pix.
x 160 pix.
= 224.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.403 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.07
Minimum - Maximum-7.3232226 - 11.443315500000001
Average (Standard dev.)0.0026982033 (±0.13986106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 224.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43827_msk_1.map
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Additional map: sharpened map

Fileemd_43827_additional_1.map
Annotationsharpened map
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Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_43827_half_map_1.map
Annotationhalf-map 1
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Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_43827_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : Fab 77-stabilized MeV F ectodomain fragment

EntireName: Fab 77-stabilized MeV F ectodomain fragment
Components
  • Complex: Fab 77-stabilized MeV F ectodomain fragment
    • Complex: Antibody 77 Fab Heavy Chain, Antibody 77 Fab Light Chain
      • Protein or peptide: mAb 77 light chain
      • Protein or peptide: mAB 77 heavy chain
    • Complex: Measles virus Fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fab 77-stabilized MeV F ectodomain fragment

SupramoleculeName: Fab 77-stabilized MeV F ectodomain fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: last refolding step of F ectodomain refolding in the presence of mAb 77
Molecular weightTheoretical: 43 KDa

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Supramolecule #2: Antibody 77 Fab Heavy Chain, Antibody 77 Fab Light Chain

SupramoleculeName: Antibody 77 Fab Heavy Chain, Antibody 77 Fab Light Chain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Measles virus Fusion glycoprotein

SupramoleculeName: Measles virus Fusion glycoprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Measles virus strain Ichinose-B95a / Strain: Ichinose-B95a

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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: Measles virus strain Ichinose-B95a
Molecular weightTheoretical: 57.379539 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG ...String:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG QGMILAVQGV QDYINNELIP SMNQLSCDLI GQKLGLKLLR YYTEILSLFG PSLRDPISAE ISIQALSYAL GG DINKVLE KLGYSGGDLL GILESRGIKA RITHVDTESY FIVLSIAYPT LSEIKGVIVH RLEGVSYNIG SQEWYTTVPK YVA TQGYLI SNFDESSCTF MPEGTVCSQN ALYPMSPLLQ ECLRGSTKSC ARTLVSGSFG NRFILSQGNL IANCASILCK CYTT GTIIN QDPDKILTYI AADHCPVVEV NGVTIQVGSR RYPDAVYLHR IDLGPPISLG RLDVGTNLGN AIAKLEDAKE LLESS DQIL RSMKGLSSTS IGVDDDDKAG WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: mAb 77 light chain

MacromoleculeName: mAb 77 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.532512 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSD VQITQSPSYL AASPGETITI NCRASKSISK YLAWYQEKPG KTNELLIYSG STLQSGIPSR FRGSGSGTD FTLTISSLEP EDFAMYYCQQ HNEYTLTFGG GTKLELKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String:
MGWSCIILFL VATATGVHSD VQITQSPSYL AASPGETITI NCRASKSISK YLAWYQEKPG KTNELLIYSG STLQSGIPSR FRGSGSGTD FTLTISSLEP EDFAMYYCQQ HNEYTLTFGG GTKLELKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: mAB 77 heavy chain

MacromoleculeName: mAB 77 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.722336 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSD VQLQESGPGL VKPSQSLSLT CTVSGYSITS DYAWNWIRQF PGNKLEWMGY ISYTLTTGYN PSLKSRISI TRDSSKNQFF LQLNSVTTED TATYYCARSG WLLPYWYFDV WGAGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSD VQLQESGPGL VKPSQSLSLT CTVSGYSITS DYAWNWIRQF PGNKLEWMGY ISYTLTTGYN PSLKSRISI TRDSSKNQFF LQLNSVTTED TATYYCARSG WLLPYWYFDV WGAGTTVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP KSCDKGL EVLFQGPTHT CPPCPAPELL GGPSVFLFPP KPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NAK TKPREE QYNSTYRVVS VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS RDELTKNQVS LTCL VKGFY PSDIAVEWES NGQPENNYKT TPPVLDSDGS FFLYSKLTVD KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.2 mg/mL
BufferpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 10344 / Average exposure time: 2.0 sec. / 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: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1000000
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2) / Number images used: 94000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC, RELION)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: RELION

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Atomic model buiding 1

Initial modelPDB ID:

5yxw


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

PDB-9at8:
Fab 77-stabilized MeV F ectodomain fragment

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