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- EMDB-70793: Human antibody Fab MPV498 bound to hMPV B2 post-fusion F -

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Basic information

Entry
Database: EMDB / ID: EMD-70793
TitleHuman antibody Fab MPV498 bound to hMPV B2 post-fusion F
Map dataMPV458-B2postF
Sample
  • Complex: MPV498 Fab bound to hMPV B2 post-fusion F protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV498 Fab heavy chain
    • Protein or peptide: MPV498 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordshMPV / Human respiratory disease / cryoem / human metapneumovirus / IMMUNE SYSTEM / ANTIVIRAL PROTEIN
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human) / human metapneumovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsGhazi Esfahani B / Mousa J / Khalil AM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI143865 United States
CitationJournal: To Be Published
Title: Human metapneumovirus-specific antibodies isolated from infected children target diverse epitopes and have prophylactic efficacy in mice
Authors: Khalil AM / Ghazi Esfahani B / Mousa J
History
DepositionMay 23, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70793.png

Downloads & links

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Map

FileDownload / File: emd_70793.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMPV458-B2postF
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 420 pix.
= 331.8 Å		0.79 Å/pix.
x 420 pix.
= 331.8 Å		0.79 Å/pix.
x 420 pix.
= 331.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.6458654 - 3.5832722
Average (Standard dev.)-0.0009465618 (±0.07553149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 331.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_70793_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70793_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70793_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 : MPV498 Fab bound to hMPV B2 post-fusion F protein

EntireName: MPV498 Fab bound to hMPV B2 post-fusion F protein
Components
  • Complex: MPV498 Fab bound to hMPV B2 post-fusion F protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV498 Fab heavy chain
    • Protein or peptide: MPV498 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: MPV498 Fab bound to hMPV B2 post-fusion F protein

SupramoleculeName: MPV498 Fab bound to hMPV B2 post-fusion F protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 421 KDa

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: human metapneumovirus
Molecular weightTheoretical: 50.664488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCTDGPSLIK TELDLTKSAL RELKTVSADQ LAREEQIENP RQSRFVLGA IALGVATAAA VTAGIAIAKT IRLESEVNAI KGALKTTNEA VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIAD ...String:
LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCTDGPSLIK TELDLTKSAL RELKTVSADQ LAREEQIENP RQSRFVLGA IALGVATAAA VTAGIAIAKT IRLESEVNAI KGALKTTNEA VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIAD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSYMPT SAGQIKLMLE NRAMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI IKAAPSCSEK DGNYACLLRE DQGWYCKNAG STVYYPNEKD CETRGDHVFC DTA AGINVA EQSRECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLP KGCSYITNQD ADTV TIDNT VYQLSKVEGE QHVIKGRPVS SSFDPIRFPE DQFNVALDQV FESIENSQAL VDQSNKILNS

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: MPV498 Fab heavy chain

MacromoleculeName: MPV498 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.434042 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIS SYYWSWIRQP AGKGLEWIGR IYTSGNTNYN PSLKSRVTMS LDTSKNQVSL KLSSVTAAD TAVYYCARSR VATTPVGLRD WLDPWGQGTL VTVSS

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Macromolecule #3: MPV498 Fab light chain

MacromoleculeName: MPV498 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.810029 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TPSLSASVGD RVTITCRASQ SISSYLNWYQ QKPGKAPKLL IYAASSLQSG VPSRFSGSGS GTDFTLTISS LQPEDFATYY CQQSYSTPL FFGQGTKLEI K

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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: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 12 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7m0i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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