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- PDB-7sco: Structure of H1 influenza hemagglutinin bound to Fab 310-39G10 -

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Basic information

Entry
Database: PDB / ID: 7sco
TitleStructure of H1 influenza hemagglutinin bound to Fab 310-39G10
Components
  • (310-39G10 Fab, ...) x 2
  • (Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN/Immune System / influenza / hemagglutinin / antibody / H1 / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsTorrents de la Pena, A. / Ward, A.B.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2022
Title: Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus.
Authors: Maya Sangesland / Alba Torrents de la Peña / Seyhan Boyoglu-Barnum / Larance Ronsard / Faez Amokrane Nait Mohamed / Thalia Bracamonte Moreno / Ralston M Barnes / Daniel Rohrer / Nils ...Authors: Maya Sangesland / Alba Torrents de la Peña / Seyhan Boyoglu-Barnum / Larance Ronsard / Faez Amokrane Nait Mohamed / Thalia Bracamonte Moreno / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Musie Ghebremichael / Masaru Kanekiyo / Andrew Ward / Daniel Lingwood /
Abstract: Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) ...Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrated that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage expandability, we compared F54 versus L54 as substrate within humanized mice, where antibodies develop with human-like CDRH3 diversity but are restricted to single V genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. Therefore, IGHV1-69 polymorphism, which is skewed ethnically, gates tolerance and vaccine expandability of influenza bnAbs.
History
DepositionSep 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: 310-39G10 Fab, Heavy Chain
L: 310-39G10 Fab, Light Chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: 310-39G10 Fab, Heavy Chain
F: 310-39G10 Fab, Light Chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA2 chain
J: 310-39G10 Fab, Heavy Chain
K: 310-39G10 Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,06627
Polymers261,13812
Non-polymers3,92815
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACGBDI

#1: Protein Hemagglutinin HA1 chain


Mass: 35932.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1)
Strain: A/New Zealand:South Canterbury/35/2000 H1N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q289M7
#2: Protein Hemagglutinin HA2 chain


Mass: 26637.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/New Zealand:South Canterbury/35/2000 H1N1)
Strain: A/New Zealand:South Canterbury/35/2000 H1N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q289M7

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Antibody , 2 types, 6 molecules HEJLFK

#3: Antibody 310-39G10 Fab, Heavy Chain


Mass: 12796.269 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#4: Antibody 310-39G10 Fab, Light Chain


Mass: 11679.963 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)

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Sugars , 2 types, 15 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of H1 NC99 influenza hemagglutinin bound to Fab 310-39G10
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: 293F
Buffer solutionpH: 7.4 / Details: TBS buffer, PH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HClTris1
2150 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: hemagglutinin at 2mg/ml is complexed with the Fab at a molar ratio 1:3 (HA:Fab). The sample is incubated for 30min at RT and diluted with TBS to a final concentration of 0.2mg/ml
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K
Details: Blotting time: 5.5 s Blotting force: 0 Waiting time: 7 s

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 10 sec. / Electron dose: 49.88 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 853

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCv3.2.0particle selectionblob picker
2Leginonimage acquisition
4Gctf1.06CTF correction
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135198 / Algorithm: BACK PROJECTION / Symmetry type: POINT

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