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- EMDB-71547: Human antibody Fab MPV513 bound to hMPV DsCav-ES2 -

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Basic information

Entry
Database: EMDB / ID: EMD-71547
TitleHuman antibody Fab MPV513 bound to hMPV DsCav-ES2
Map data
Sample
  • Complex: MPV513 Fab bound to hMPV DsCav-ES2 F protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV513 Heavy Chain
    • Protein or peptide: MPV513 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: 3.94 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)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_71547.png

Downloads & links

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Map

FileDownload / File: emd_71547.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.)
0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.5094576 - 1.7648897
Average (Standard dev.)0.0003831654 (±0.030819928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 246.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened by deepEMhancer

Fileemd_71547_additional_1.map
Annotationsharpened by deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: MPV499- hMPV DsCav-ES2

Fileemd_71547_additional_2.map
AnnotationMPV499- hMPV DsCav-ES2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_71547_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_71547_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MPV513 Fab bound to hMPV DsCav-ES2 F protein

EntireName: MPV513 Fab bound to hMPV DsCav-ES2 F protein
Components
  • Complex: MPV513 Fab bound to hMPV DsCav-ES2 F protein
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: MPV513 Heavy Chain
    • Protein or peptide: MPV513 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: MPV513 Fab bound to hMPV DsCav-ES2 F protein

SupramoleculeName: MPV513 Fab bound to hMPV DsCav-ES2 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: 1 / Enantiomer: LEVO
Source (natural)Organism: human metapneumovirus
Molecular weightTheoretical: 44.717039 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 VYQLSKV

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: MPV513 Heavy Chain

MacromoleculeName: MPV513 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.402724 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSGAE VKKPGESLRI SCKGSGYDFP SYWISWVRQM PGKGLEWMGR IDPTDSNTNY SPSFQGHVTL SADKSISTAY LQWSSLKAS DTAIYYCARH SDSWSYYEDS WGQGTLVTVS S

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Macromolecule #3: MPV513 Light Chain

MacromoleculeName: MPV513 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.724072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGRLSGTD FTLTISSLQP EDFATYYCQ QTYSSPRTFG QGTKVEIK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 204000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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