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- EMDB-71548: Human antibody Fab MPV510 bound to hMPV DsCav-ES2-IPDS F protein -

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Basic information

Entry
Database: EMDB / ID: EMD-71548
TitleHuman antibody Fab MPV510 bound to hMPV DsCav-ES2-IPDS F protein
Map data
Sample
  • Complex: MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV510 Fab heavy chain
    • Protein or peptide: MPV510 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordshMPV / Human respiratory disease / cryoem / human metapneumovirus / VIRAL PROTEIN-IMMUNE SYSTEM complex
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: 2.85 Å
AuthorsGhazi Esfahani N / 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)R01 AI143865 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
DepositionJul 1, 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_71548.png

Downloads & links

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Map

FileDownload / File: emd_71548.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 280 pix.
= 221. Å		0.79 Å/pix.
x 280 pix.
= 221. Å		0.79 Å/pix.
x 280 pix.
= 221. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78929 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.5014267 - 0.72790325
Average (Standard dev.)0.00074637675 (±0.02292521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 221.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71548_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_71548_half_map_1.map
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71548_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F

EntireName: MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F
Components
  • Complex: MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV510 Fab heavy chain
    • Protein or peptide: MPV510 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F

SupramoleculeName: MPV510 Fab bound to hMPV DsCav-ES2-IPDS pre-fusion F / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human metapneumovirus
Molecular weightTheoretical: 48.948984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTCSADQ LAREEQIENP RQSRFVLGA IACGVATAAA VTAGVAIAKC IRLESEVTAI KNCLKKTNEC VSTLGCGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD ...String:
LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTCSADQ LAREEQIENP RQSRFVLGA IACGVATAAA VTAGVAIAKC IRLESEVTAI KNCLKKTNEC VSTLGCGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISKDLMTDAE LARAISNMPT SAGQIKLMLE NRCMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI VKAAPSCSEK KGNYACLLRE DQGWYCQNAG STVYYPCEKD CETRGDHVFC DTA AGINVA EQSKECNINI STTNYPCKVS CGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLN KGCSYITNQD ADTV TIDNT VYQLSKVEGE QHVIKGRPVS SSFDPVKFPQ DQFNVALDQC FES

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: MPV510 Fab heavy chain

MacromoleculeName: MPV510 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.268489 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGSG LVKPSQTLSL TCAVSGGSIS SGDSSWSWIR QPPGKGLEWI GHVYESGNTY YDPSLQSRVT ISVDRSRNQF SLKLTSVTV ADTAVYYCAR EGNYGWDYFD YWGQGTLVTV SS

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Macromolecule #3: MPV510 Fab light chain

MacromoleculeName: MPV510 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.782163 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTSPFSL SASVGDRVTI TCRASQSINS YLNWYQQKPG KAPRLLIYAA SSLQSGVPSR FRGSGSGTDF ALTISSLQPE DFATYYCQQ SYRPPSRTFG QGTKVEMK

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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: 6 / 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

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:

7ur4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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