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- EMDB-26983: 1F8 mAb in complex with the computationally optimized broadly rea... -

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Basic information

Entry
Database: EMDB / ID: EMD-26983
Title1F8 mAb in complex with the computationally optimized broadly reactive H1 influenza hemagglutinin P1
Map dataCryoEM map of COBRA P1 HA in complex with 1F8 mAb
Sample
  • Complex: COBRA P1 HA in complex with 1F8 mAb
    • Complex: COBRA P1 hemagglutinin
      • Protein or peptide: COBRA P1 HA
    • Complex: 1F8 monoclonal antibody
      • Protein or peptide: 1F8 light chain
      • Protein or peptide: 1F8 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / influenza virus / COBRA / monoclonal antibody / IMMUNE SYSTEM / Viral Protein-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Influenza A virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDzimianski JV / DuBois RM / Ward A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Commun Biol / Year: 2023
Title: Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine.
Authors: John V Dzimianski / Julianna Han / Giuseppe A Sautto / Sara M O'Rourke / Joseph M Cruz / Spencer R Pierce / Jeffrey W Ecker / Michael A Carlock / Kaito A Nagashima / Jarrod J Mousa / Ted M ...Authors: John V Dzimianski / Julianna Han / Giuseppe A Sautto / Sara M O'Rourke / Joseph M Cruz / Spencer R Pierce / Jeffrey W Ecker / Michael A Carlock / Kaito A Nagashima / Jarrod J Mousa / Ted M Ross / Andrew B Ward / Rebecca M DuBois /
Abstract: Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally ...Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding.
History
DepositionMay 13, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26983.png

Downloads & links

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Map

FileDownload / File: emd_26983.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of COBRA P1 HA in complex with 1F8 mAb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.73570263 - 1.626761
Average (Standard dev.)-0.00046894228 (±0.03625338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26983_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map B of COBRA P1 HA in complex with 1F8 mAb

Fileemd_26983_half_map_1.map
AnnotationCryoEM half map B of COBRA P1 HA in complex with 1F8 mAb
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map A of COBRA P1 HA in complex with 1F8 mAb

Fileemd_26983_half_map_2.map
AnnotationCryoEM half map A of COBRA P1 HA in complex with 1F8 mAb
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : COBRA P1 HA in complex with 1F8 mAb

EntireName: COBRA P1 HA in complex with 1F8 mAb
Components
  • Complex: COBRA P1 HA in complex with 1F8 mAb
    • Complex: COBRA P1 hemagglutinin
      • Protein or peptide: COBRA P1 HA
    • Complex: 1F8 monoclonal antibody
      • Protein or peptide: 1F8 light chain
      • Protein or peptide: 1F8 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: COBRA P1 HA in complex with 1F8 mAb

SupramoleculeName: COBRA P1 HA in complex with 1F8 mAb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: COBRA P1 hemagglutinin

SupramoleculeName: COBRA P1 hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: HA antigen designed from human H1N1 viruses from 1933-1957 and 2009-2011, and swine H1N1 viruses from 1931-1998.
Source (natural)Organism: Influenza A virus

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Supramolecule #3: 1F8 monoclonal antibody

SupramoleculeName: 1F8 monoclonal antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Details: Recombinantly expressed Fab fragment of an IgG antibody.
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: COBRA P1 HA

MacromoleculeName: COBRA P1 HA / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 63.264535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCKLKGIAPL QLGKCNIAGW LLGNPECESL LSARSWSYIV ETPNSENGT CYPGDFIDYE ELREQLSSVS SFERFEIFPK ESSWPNHNTT KGVTAACSHA GKSSFYRNLL WLTKKGGSYP K LSKSYVNN ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCKLKGIAPL QLGKCNIAGW LLGNPECESL LSARSWSYIV ETPNSENGT CYPGDFIDYE ELREQLSSVS SFERFEIFPK ESSWPNHNTT KGVTAACSHA GKSSFYRNLL WLTKKGGSYP K LSKSYVNN KGKEVLVLWG VHHPSTSTDQ QSLYQNENAY VSVVSSNYNR RFTPEIAERP KVRGQAGRMN YYWTLLEPGD TI IFEATGN LIAPWYAFAL SRGSGSGIIT SNASMHECNT KCQTPQGAIN SSLPFQNIHP VTIGECPKYV RSTKLRMVTG LRN IPSIQS RGLFGAIAGF IEGGWTGMID GWYGYHHQNE QGSGYAADQK STQNAINGIT NKVNSVIEKM NTQFTAVGKE FNNL EKRME NLNKKVDDGF LDIWTYNAEL LVLLENERTL DFHDSNVKNL YEKVKSQLRN NAKEIGNGCF EFYHKCDNEC MESVK NGTY DYPKYSEESK LNREKIDGVK LESMGVYGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGLND IFEAQKIEWH EGHHHH HH

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Macromolecule #2: 1F8 light chain

MacromoleculeName: 1F8 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.918271 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVLTQSPAS LAVSLGQRAT ISCKASQSVD FDGDTYMSWY QQKPGQPPKL LIYAASKLES GIPARFSGSG SGTDFTLNIH PVEEEDAAT YFCQQSNEDP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPAS LAVSLGQRAT ISCKASQSVD FDGDTYMSWY QQKPGQPPKL LIYAASKLES GIPARFSGSG SGTDFTLNIH PVEEEDAAT YFCQQSNEDP WTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNEC

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Macromolecule #3: 1F8 heavy chain

MacromoleculeName: 1F8 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.900818 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLQQSGAE LMKPGASVKI SCKATGYTFS SYWIEWVKQR PGHGLEWIGE ILPGSGRTNY DERFKGKATF TADTSSNTAY MQLSSLTSE DSAVYYCARP RIYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH ...String:
QVQLQQSGAE LMKPGASVKI SCKATGYTFS SYWIEWVKQR PGHGLEWIGE ILPGSGRTNY DERFKGKATF TADTSSNTAY MQLSSLTSE DSAVYYCARP RIYGMDYWGQ GTSVTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVP SSPRPSETVT CNVAHPASST KVDKKIEPRG LVPR

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 10 / 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

Concentration0.8 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details1:3:3 molar ratio of P1 HA, 1F8, and P1-05

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57151
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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