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- EMDB-45412: Cryo-EM Structure of the Human Neutralizing Antibody 5-1 in Compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-45412
TitleCryo-EM Structure of the Human Neutralizing Antibody 5-1 in Complex with Prefusion Human Metapneumovirus F Glycoprotein
Map dataunsharpend EM Map
Sample
  • Complex: The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab
    • Complex: hMPV F-DsCavEs2-IPDS Trimer
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5-1 Fab Heavy chain Variable Domain
      • Protein or peptide: 5-1 Fab Heavy Chain Variable Domain
    • Complex: 5-1 Fab Light Chain Variable Domain
      • Protein or peptide: 5-1 Fab Light Chain Variable Domain
KeywordshMPV F / 5-1 antibody / antibody / VIRAL PROTEIN-IMMUNE SYSTEM / 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 specieshuman metapneumovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.24 Å
AuthorsGuo LQ / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Potent cross-neutralizing RSV/hMPV antibody targeting antigenic site V
Authors: Abu-Shmais AA / Guo LQ / Miller RJ / Janke JK / Vukovich MJ / Lindsay EB / Rush SA / Wolter RM / Kose N / Carnahan RH / Crowe JE / Bonami RH / Mousa JJ / McLellan JS / Georgiev IS
History
DepositionJun 18, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45412.png

Downloads & links

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Map

FileDownload / File: emd_45412.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpend EM Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å		0.94 Å/pix.
x 360 pix.
= 338.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0251
Minimum - Maximum-0.023329774 - 0.08218152
Average (Standard dev.)-0.000050723298 (±0.0035138733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 338.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45412_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened EM map by DeepEMhancer

Fileemd_45412_additional_1.map
AnnotationSharpened EM map by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45412_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_45412_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 : The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab

EntireName: The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab
Components
  • Complex: The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab
    • Complex: hMPV F-DsCavEs2-IPDS Trimer
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5-1 Fab Heavy chain Variable Domain
      • Protein or peptide: 5-1 Fab Heavy Chain Variable Domain
    • Complex: 5-1 Fab Light Chain Variable Domain
      • Protein or peptide: 5-1 Fab Light Chain Variable Domain

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Supramolecule #1: The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab

SupramoleculeName: The protein complex of hMPV F-DsCavEs2-IPDS and 5-1 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: hMPV F-DsCavEs2-IPDS Trimer

SupramoleculeName: hMPV F-DsCavEs2-IPDS Trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: human metapneumovirus

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Supramolecule #3: 5-1 Fab Heavy chain Variable Domain

SupramoleculeName: 5-1 Fab Heavy chain Variable Domain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 5-1 Fab Light Chain Variable Domain

SupramoleculeName: 5-1 Fab Light Chain Variable Domain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 5-1 Fab Heavy Chain Variable Domain

MacromoleculeName: 5-1 Fab Heavy Chain Variable Domain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.170996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGQLVQSGPE VKKPGATVKV SCRASAYPFG NYGITWVRQV PGQGLEWVGW ISAYTGHTKF PQNFQGRVTL TADTSTSTGY MELRSLTSD DTAVYYCARG PCCSSPRPYD IWGQGTMVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QGQLVQSGPE VKKPGATVKV SCRASAYPFG NYGITWVRQV PGQGLEWVGW ISAYTGHTKF PQNFQGRVTL TADTSTSTGY MELRSLTSD DTAVYYCARG PCCSSPRPYD IWGQGTMVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK V

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Macromolecule #2: 5-1 Fab Light Chain Variable Domain

MacromoleculeName: 5-1 Fab Light Chain Variable Domain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.586084 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASVGDRVT ITCRASQSID DWLAWYQHSP GKAPKLLIYR ASRLESGVPS RFSGSGSGTE FTLTISSLQP DDFASYYCQ QCYTYSQTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPST LSASVGDRVT ITCRASQSID DWLAWYQHSP GKAPKLLIYR ASRLESGVPS RFSGSGSGTE FTLTISSLQP DDFASYYCQ QCYTYSQTFG QGTRVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human metapneumovirus
Molecular weightTheoretical: 60.48993 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTCSADQL AREEQIENPR RRRFVLGAIA CGVATAAAVT AGVAIAKCIR LESEVTAIKN CLKKTNECVS TLGCGVRVLA T AVRELKDF ...String:
MSWKVVIIFS LLITPQHGLK ESYLEESCST ITEGYLSVLR TGWYTNVFTL EVGDVENLTC ADGPSLIKTE LDLTKSALRE LRTCSADQL AREEQIENPR RRRFVLGAIA CGVATAAAVT AGVAIAKCIR LESEVTAIKN CLKKTNECVS TLGCGVRVLA T AVRELKDF VSKNLTRAIN KNKCDIPDLK MAVSFSQFNR RFLNVVRQFS DNAGITPAIS KDLMTDAELA RAISNMPTSA GQ IKLMLEN RCMVRRKGFG ILIGVYGSSV IYMVQLPIFG VIDTPCWIVK AAPSCSEKKG NYACLLREDQ GWYCQNAGST VYY PCEKDC ETRGDHVFCD TAAGINVAEQ SKECNINIST TNYPCKVSCG RHPISMVALS PLGALVACYK GVSCSIGSNR VGII KQLNK GCSYITNQDA DTVTIDNTVY QLSKVEGEQH VIKGRPVSSS FDPVKFPQDQ FNVALDQCFE SIENSQALVD QSNRI LSSA EKGNTGGGGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEK

UniProtKB: Fusion glycoprotein F0

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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: 7.4 / Details: PBS, pH 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 13.2 sec. / Average electron dose: 48.64 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18483
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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