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- PDB-7l0l: Cryo-EM structure of the VRC316 clinical trial, vaccine-elicited,... -

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Basic information

Entry
Database: PDB / ID: 7l0l
TitleCryo-EM structure of the VRC316 clinical trial, vaccine-elicited, human antibody 316-310-1B11 in complex with an H2 CAN05 HA trimer
Components
  • 316-310-1B11 Heavy Chain
  • 316-310-1B11 Light Chain
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsIMMUNE SYSTEM/Viral protein / VRC / IMMUNE SYSTEM / VRC316 / H2 / Fab / Flu / IMMUNE SYSTEM-Viral protein 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: 2.85 Å
AuthorsGorman, J. / Kwong, P.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247) United States
CitationJournal: Nat Med / Year: 2022
Title: A single residue in influenza virus H2 hemagglutinin enhances the breadth of the B cell response elicited by H2 vaccination.
Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R ...Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R Harris / Adam S Olia / Alexandra F Nazzari / Tongqing Zhou / Katherine V Houser / Grace L Chen / John R Mascola / Barney S Graham / Masaru Kanekiyo / Julie E Ledgerwood / Peter D Kwong / Adrian B McDermott /
Abstract: Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem- ...Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem-specific epitopes have been extensively characterized for HA subtypes H1 and H5 in humans. H2N2 influenza virus circulated 50 years ago and represents a pandemic threat due to the lack of widespread immunity, but, unlike H1 and H5, the H2 HA stem contains Phe45 predicted to sterically clash with HA stem-binding antibodies characterized to date. To understand the effect of Phe45, we compared the HA stem-specific B cell response in post hoc analyses of two phase 1 clinical trials, one testing vaccination with an H2 ferritin nanoparticle immunogen ( NCT03186781 ) and one with an inactivated H5N1 vaccine ( NCT01086657 ). In H2-naive individuals, the magnitude of the B cell response was equivalent, but H2-elicited HA stem-binding B cells displayed greater cross-reactivity than those elicited by H5. However, in individuals with childhood H2 exposure, H5-elicited HA stem-binding B cells also displayed high cross-reactivity, suggesting recall of memory B cells formed 50 years ago. Overall, we propose that a one-residue difference on an HA immunogen can alter establishment and expansion of broadly neutralizing memory B cells. These data have implications for stem-based universal influenza vaccination strategies.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-23098
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Structure viewerMolecule:
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Assembly

Deposited unit
L: 316-310-1B11 Light Chain
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
H: 316-310-1B11 Heavy Chain
J: 316-310-1B11 Light Chain
C: Hemagglutinin HA1 chain
E: Hemagglutinin HA2 chain
G: 316-310-1B11 Heavy Chain
K: 316-310-1B11 Light Chain
D: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
I: 316-310-1B11 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,76827
Polymers338,45012
Non-polymers3,31815
Water00
1


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

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Components

#1: Antibody 316-310-1B11 Light Chain


Mass: 23460.025 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: Protein Hemagglutinin HA1 chain


Mass: 38802.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Canada/720/2005(H2N2))
Strain: A/Canada/720/2005(H2N2) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q4ZH98
#3: Protein Hemagglutinin HA2 chain


Mass: 25489.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Canada/720/2005(H2N2))
Strain: A/Canada/720/2005(H2N2) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q4ZH98
#4: Antibody 316-310-1B11 Heavy Chain


Mass: 25065.092 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / 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
Has protein modificationY

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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: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer componentFormula: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Cryo-EM structure of the VRC316 clinical trial, vaccine-elicited, human antibody 316-310-1B11 in complex with an H2 CAN05 HA trimer
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K

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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 FIELD / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51.16 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2439
Image scansMovie frames/image: 50

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
11cryoSPARC2.12classification
12cryoSPARC2.153D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115194 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13KU3

3ku3

13KU31PDBexperimental model
21
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317595
ELECTRON MICROSCOPYf_angle_d0.44523817
ELECTRON MICROSCOPYf_dihedral_angle_d3.8262436
ELECTRON MICROSCOPYf_chiral_restr0.0422598
ELECTRON MICROSCOPYf_plane_restr0.0043075

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