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- PDB-8tnl: CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 i... -

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Basic information

Entry
Database: PDB / ID: 8tnl
TitleCryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
Components
  • (H7.HK1 Neutralizing Antibody Heavy Chain) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / virus / antibody / influenza / 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 / apical plasma membrane / 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
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 speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsMorano, N.C. / Wu, X. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationPG010737 United States
CitationJournal: To Be Published
Title: CryoEM structure of H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
Authors: Morano, N.C. / Wu, X. / Shapiro, L.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: H7.HK1 Neutralizing Antibody Heavy Chain
L: H7.HK1 Neutralizing Antibody Heavy Chain
C: Hemagglutinin
I: Hemagglutinin
K: Hemagglutinin
D: H7.HK1 Neutralizing Antibody Heavy Chain
E: H7.HK1 Neutralizing Antibody Heavy Chain
A: H7.HK1 Neutralizing Antibody Heavy Chain
B: H7.HK1 Neutralizing Antibody Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,80516
Polymers264,2579
Non-polymers1,5487
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody H7.HK1 Neutralizing Antibody Heavy Chain


Mass: 12856.218 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody H7.HK1 Neutralizing Antibody Heavy Chain


Mass: 12153.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Hemagglutinin /


Mass: 63075.688 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9))
Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A0A067Y6L0
#4: 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.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
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
Has ligand of interestN

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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: H7 hemagglutinin from A/Shanghai2/2013 H7N9 in complex with a human neutralizing antibody H7.HK1
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.06 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178347 / Symmetry type: POINT

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