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- EMDB-27920: 3H03 Fab in complex with influenza virus neuraminidase from A/Bre... -

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Basic information

Entry
Database: EMDB / ID: EMD-27920
Title3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
Map datasharpened map
Sample
  • Complex: 3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: 3H03 fragment antigen binding light chain
    • Protein or peptide: 3H03 fragment antigen binding heavy chain
Keywordsinfluenza / monoclonal antibody / NA / H1N1 / cross-reactive antibody / VIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/Brevig Mission/1/1918(H1N1)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsTurner HL / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93109C00051 United States
CitationJournal: Immunity / Year: 2023
Title: Human anti-N1 monoclonal antibodies elicited by pandemic H1N1 virus infection broadly inhibit HxN1 viruses in vitro and in vivo.
Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / ...Authors: Lena Hansen / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Jackson S Turner / Gabriel Ozorowski / Daniel Stadlbauer / Juha Vahokoski / Aaron J Schmitz / Amena A Rizk / Wafaa B Alsoussi / Shirin Strohmeier / Wenli Yu / José Alberto Choreño-Parra / Luis Jiménez-Alvarez / Alfredo Cruz-Lagunas / Joaquín Zúñiga / Philip A Mudd / Rebecca J Cox / Ian A Wilson / Andrew B Ward / Ali H Ellebedy / Florian Krammer /
Abstract: Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA ...Neuraminidase (NA) is one of the two influenza virus surface glycoproteins, and antibodies that target it are an independent correlate of protection. However, our current understanding of NA antigenicity is incomplete. Here, we describe human monoclonal antibodies (mAbs) from a patient with a pandemic H1N1 virus infection in 2009. Two mAbs exhibited broad reactivity and inhibited NA enzyme activity of seasonal H1N1 viruses circulating before and after 2009, as well as viruses with avian or swine N1s. The mAbs provided robust protection from lethal challenge with human H1N1 and avian H5N1 viruses in mice, and both target an epitope on the lateral face of NA. In summary, we identified two broadly protective NA antibodies that share a novel epitope, inhibited NA activity, and provide protection against virus challenge in mice. Our work reaffirms that NA should be included as a target in future broadly protective or universal influenza virus vaccines.
History
DepositionAug 22, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27920.png

Downloads & links

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Map

FileDownload / File: emd_27920.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 290. Å		0.73 Å/pix.
x 400 pix.
= 290. Å		0.73 Å/pix.
x 400 pix.
= 290. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.71443117 - 1.0159844
Average (Standard dev.)0.00040005695 (±0.030910933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 290.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27920_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_27920_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_27920_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 3H03 Fab in complex with influenza virus neuraminidase from A/Bre...

EntireName: 3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
Components
  • Complex: 3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: 3H03 fragment antigen binding light chain
    • Protein or peptide: 3H03 fragment antigen binding heavy chain

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Supramolecule #1: 3H03 Fab in complex with influenza virus neuraminidase from A/Bre...

SupramoleculeName: 3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1)) / Strain: A/Brevig Mission/1/1918 H1N1
Molecular weightTheoretical: 49.726387 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RSVILTGNSS LCPISGWAIY SKDNGIRIG SKGDVFVIRE PFISCSHLEC RTFFLTQGAL LNDKHSNGTV KDRSPYRTLM SCPVGEAPSP YNSRFESVAW S ASACHDGM ...String:
ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RSVILTGNSS LCPISGWAIY SKDNGIRIG SKGDVFVIRE PFISCSHLEC RTFFLTQGAL LNDKHSNGTV KDRSPYRTLM SCPVGEAPSP YNSRFESVAW S ASACHDGM GWLTIGISGP DNGAVAVLKY NGIITDTIKS WRNNILRTQE SECACVNGSC FTIMTDGPSN GQASYKILKI EK GKVTKSI ELNAPNYHYE ECSCYPDTGK VMCVCRDNWH GSNRPWVSFD QNLDYQIGYI CSGVFGDNPR PNDGTGSCGP VSS NGANGI KGFSFRYDNG VWIGRTKSTS SRSGFEMIWD PNGWTETDSS FSVRQDIVAI TDWSGYSGSF VQHPELTGLD CMRP CFWVE LIRGQPKENT IWTSGSSISF CGVNSDTVGW SWPDGAELPF SIDK

UniProtKB: Neuraminidase

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Macromolecule #2: 3H03 fragment antigen binding light chain

MacromoleculeName: 3H03 fragment antigen binding light chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.361855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSTSVGDRVT ITCRASQTIS TYLNWYQQKP GKAPELLIYV ASSLQSGVPS RFSGTGSGTE FTLTISSLQP GDFATYYCQ QSYSSPFTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSTSVGDRVT ITCRASQTIS TYLNWYQQKP GKAPELLIYV ASSLQSGVPS RFSGTGSGTE FTLTISSLQP GDFATYYCQ QSYSSPFTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: 3H03 fragment antigen binding heavy chain

MacromoleculeName: 3H03 fragment antigen binding heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.484332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGDSIS SSYYYWGWIR QSPVKGLEWI GSFFYSGNTN YNPSLKSRVT ISVDTSKNQF SLNLRSVTA ADTAVYYCAR HVTSISSWNR GVYLDSWGRG ALVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLQESGPG LVKPSETLSL TCTVSGDSIS SSYYYWGWIR QSPVKGLEWI GSFFYSGNTN YNPSLKSRVT ISVDTSKNQF SLNLRSVTA ADTAVYYCAR HVTSISSWNR GVYLDSWGRG ALVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS C

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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

Concentration1.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaCl
12.0 mMOctyl-beta-glucoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 3862 / Average exposure time: 7.51 sec. / Average electron dose: 41.1 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab initio model
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 37387
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3beq


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8e6j:
3H03 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1)

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