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- EMDB-46994: Cryo-EM structure of the SFV009 3G01 Fab in complex with A/Califo... -

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Basic information

Entry
Database: EMDB / ID: EMD-46994
TitleCryo-EM structure of the SFV009 3G01 Fab in complex with A/California/04/2009
Map data
Sample
  • Complex: Hemagglutinin CA09 homotrimer bound to anchor fab
    • Complex: Fab
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
    • Complex: Hemagglutinin HA1/2
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / HA / antibody / anchor epitope / influenza virus / IMMUNE SYSTEM
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus (A/California/04/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFernandez Quintero ML / Ferguson JA / Han J / Ward AB
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: Nat Commun / Year: 2025
Title: Structurally convergent antibodies derived from different vaccine strategies target the influenza virus HA anchor epitope with a subset of V3 and V3 genes.
Authors: Ting-Hui Lin / Chang-Chun David Lee / Monica L Fernández-Quintero / James A Ferguson / Julianna Han / Xueyong Zhu / Wenli Yu / Jenna J Guthmiller / Florian Krammer / Patrick C Wilson / ...Authors: Ting-Hui Lin / Chang-Chun David Lee / Monica L Fernández-Quintero / James A Ferguson / Julianna Han / Xueyong Zhu / Wenli Yu / Jenna J Guthmiller / Florian Krammer / Patrick C Wilson / Andrew B Ward / Ian A Wilson /
Abstract: H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine ...H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine to elicit broadly neutralizing antibodies (bnAbs). Identification and characterization of bnAbs elicited in natural infection and immunization to influenza virus hemagglutinin (HA) can provide insights for development of a universal influenza vaccine. Here, we structurally and biophysically characterize four antibodies that bind to a conserved region on the HA membrane-proximal region known as the anchor epitope. Despite some diversity in their V and V genes, the antibodies interact with the HA through germline-encoded residues in HCDR2 and LCDR3. Somatic mutations on HCDR3 also contribute hydrophobic interactions with the conserved HA epitope. This convergent binding mode provides extensive neutralization breadth against H1N1 viruses and suggests possible countermeasures against H1N1 viruses.
History
DepositionSep 11, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46994.png

Downloads & links

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Map

FileDownload / File: emd_46994.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.101
Minimum - Maximum-0.45619914 - 0.70328796
Average (Standard dev.)-0.0000083736895 (±0.0146011785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46994_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46994_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 : Hemagglutinin CA09 homotrimer bound to anchor fab

EntireName: Hemagglutinin CA09 homotrimer bound to anchor fab
Components
  • Complex: Hemagglutinin CA09 homotrimer bound to anchor fab
    • Complex: Fab
      • Protein or peptide: Fab light chain
      • Protein or peptide: Fab heavy chain
    • Complex: Hemagglutinin HA1/2
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hemagglutinin CA09 homotrimer bound to anchor fab

SupramoleculeName: Hemagglutinin CA09 homotrimer bound to anchor fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Fab

SupramoleculeName: Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2

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Supramolecule #3: Hemagglutinin HA1/2

SupramoleculeName: Hemagglutinin HA1/2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4

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Macromolecule #1: Fab light chain

MacromoleculeName: Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.803136 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASESVS TYLAWYQKKP GQAPRLLIYD ASHRATGIPA RFSGSGSGTD FTLTISSLES EDFGVYYCQ QRSNWPPITF GQGTRLEIK

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Macromolecule #2: Fab heavy chain

MacromoleculeName: Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.490038 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFTFR IYAMHWVRQA PGKGLEWVAV ISNEGTNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRPE DAAVYYCARD PSNPPHWGNF DSWGQGTLVT VSS

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 35.960562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETPSSDNG TCYPGDFIDY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLSKSYIN ...String:
GDTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETPSSDNG TCYPGDFIDY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLSKSYIN DKGKEVLVLW GIHHPSTSAD QQSLYQNADT YVFVGSSRYS KKFKPEIAIR PKVRDQEGRM NYYWTLVEPG DK ITFEATG NLVVPRYAFA MERNAGSGII ISDTPVHDCN TTCQTPKGAI NTSLPFQNIH PITIGKCPKY VKSTKLRLAT GLR NIPS

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 26.516307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVD DGFLDIWTYN AELLVLLENE RTLDYHDSNV KNLYEKVRSQ LKNNAKEIGN GCFEFYHKCD NTCMESVKNG T YDYPKYSE ...String:
IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVD DGFLDIWTYN AELLVLLENE RTLDYHDSNV KNLYEKVRSQ LKNNAKEIGN GCFEFYHKCD NTCMESVKNG T YDYPKYSE EAKLNREEID GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH

UniProtKB: Hemagglutinin

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 15 / 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

Concentration0.7 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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) / Number grids imaged: 1 / Number real images: 3150 / Average electron dose: 44.94 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: 1.5 µm / Nominal defocus min: 0.8 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 reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.1.2) / Number images used: 90138
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChainDetails

4m4y

source_name: PDB, initial_model_type: experimental modelUsed for modelling HA
source_name: Other, initial_model_type: in silico modelFab initial model was built with Abodybuilder2
Output model

PDB-9dm0:
Cryo-EM structure of the SFV009 3G01 Fab in complex with A/California/04/2009

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