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- EMDB-28891: cryo-EM structure of a structurally designed Human metapneumoviru... -

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Basic information

Entry
Database: EMDB / ID: EMD-28891
Titlecryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8
Map datacryo-EM map for HMPV F in complex with scFv MPE8
Sample
  • Complex: Purified complex of HMPV F with single chain Fv MPE8
    • Protein or peptide: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
    • Protein or peptide: MPE8 Single chain variable fragment
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsmetapneumovirus / HMPV / F protein / antibody / MPE8 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Fusion glycoprotein F0
Similarity search - Component
Biological speciesEscherichia phage T2 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhou T / Kwong PD / Morano NC / Ou L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8
Authors: Ou L / Kwong PD
History
DepositionNov 17, 2022-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28891.png

Downloads & links

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Map

FileDownload / File: emd_28891.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map for HMPV F in complex with scFv MPE8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.281
Minimum - Maximum-0.18935351 - 0.8135917
Average (Standard dev.)0.005149258 (±0.03589117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28891_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryo-EM map for HMPV F in complex with scFv MPE8

Fileemd_28891_additional_1.map
AnnotationSharpened cryo-EM map for HMPV F in complex with scFv MPE8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map for HMPV F in complex with scFv MPE8

Fileemd_28891_half_map_1.map
Annotationcryo-EM half map for HMPV F in complex with scFv MPE8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryo-EM half map for HMPV F in complex with scFv MPE8

Fileemd_28891_half_map_2.map
Annotationcryo-EM half map for HMPV F in complex with scFv MPE8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified complex of HMPV F with single chain Fv MPE8

EntireName: Purified complex of HMPV F with single chain Fv MPE8
Components
  • Complex: Purified complex of HMPV F with single chain Fv MPE8
    • Protein or peptide: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
    • Protein or peptide: MPE8 Single chain variable fragment
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Purified complex of HMPV F with single chain Fv MPE8

SupramoleculeName: Purified complex of HMPV F with single chain Fv MPE8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 266 KDa

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Macromolecule #1: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin

MacromoleculeName: Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T2 (virus)
Molecular weightTheoretical: 56.891637 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSWKVMIIIS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC TDGPSLIKTE LDLTKSALRE LKTCSADQG SGGSGATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIPD ...String:
MSWKVMIIIS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC TDGPSLIKTE LDLTKSALRE LKTCSADQG SGGSGATAAA VTAGIAIAKT IRLESEVNAI KGCLKTTNEC VSTLGNGVRV LATAVRELKE FVSKNLTSAI N KNKCDIPD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSYMPT SAGQIKLMLE NRCMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI IKAAPSCSEK DGNYACLLRE DQGWYCKNAG STVYYPNDKD CETRGDHVFC DTA AGINVA EQSRECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLP KGCSYITNQD ADTV TIDNT VYQLSKVEGE QHVIKGRPVS SSFDPIKFPE CQFNCALDQV FESIENSQAL VDQSNKILNS AESAIGGYIP EAPRD GQAY VRKDGEWVLL STFLGGLVPR GSHHHHHHSA WSHPQFEK

UniProtKB: Fusion glycoprotein F0, Fusion glycoprotein F0, Fibritin

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Macromolecule #2: MPE8 Single chain variable fragment

MacromoleculeName: MPE8 Single chain variable fragment / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.012062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEGVQCE VQLVESGGGL VKPGGSLRLS CAASGFTFSS YSMNWVRQAP GKGLEWVSSI SASSSYSDYA DSAKGRFTI SRDNAKTSLF LQMNSLRAED TAIYFCARAR ATGYSSITPY FDIWGQGTLV TVSSGTGGSG GGGSGGGGSG G GASQSVVT ...String:
MELGLRWVFL VAILEGVQCE VQLVESGGGL VKPGGSLRLS CAASGFTFSS YSMNWVRQAP GKGLEWVSSI SASSSYSDYA DSAKGRFTI SRDNAKTSLF LQMNSLRAED TAIYFCARAR ATGYSSITPY FDIWGQGTLV TVSSGTGGSG GGGSGGGGSG G GASQSVVT QTPSVSGAPG QRVTISCTGS SSNIGAGYDV HWYQQLPGTA PKLLIYDNNN RPSGVPDRFS ASKSGTSASL AI TGLQAED EADYYCQSYD RNLSGVFGTG TKVTVLGSGE NLYFQSGGSG GHHHHHHHHS AWSHPQFEK

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / 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

Concentration0.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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:

7lze

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 192259
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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