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- PDB-7umm: H1 Solomon Islands 2006 hemagglutinin in complex with Ab109 -

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Basic information

Entry
Database: PDB / ID: 7umm
TitleH1 Solomon Islands 2006 hemagglutinin in complex with Ab109
Components
  • Hemagglutinin
  • ab109 Fab heavy chain
  • ab109 Fab light chain
KeywordsVIRAL PROTEIN / influenza / antibody / vaccine
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 speciesInfluenza A virus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsWindsor, I.W. / Caradonna, T.M. / Schmidt, A.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
CitationJournal: Cell Rep / Year: 2022
Title: An epitope-enriched immunogen expands responses to a conserved viral site.
Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa ...Authors: Timothy M Caradonna / Larance Ronsard / Ashraf S Yousif / Ian W Windsor / Rachel Hecht / Thalia Bracamonte-Moreno / Anne A Roffler / Max J Maron / Daniel P Maurer / Jared Feldman / Elisa Marchiori / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Thomas H Oguin / Gregory D Sempowski / Thomas B Kepler / Masayuki Kuraoka / Daniel Lingwood / Aaron G Schmidt /
Abstract: Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting ...Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
History
DepositionApr 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
H: ab109 Fab heavy chain
I: ab109 Fab heavy chain
J: ab109 Fab heavy chain
L: ab109 Fab light chain
M: ab109 Fab light chain
N: ab109 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,64618
Polymers317,0469
Non-polymers2,6009
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_1ens_2chain "J"
d_2ens_2chain "I"
d_3ens_2chain "H"
d_1ens_3chain "M"
d_2ens_3chain "L"
d_3ens_3chain "N"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRASPB1 - 341
d_12ens_1NAGNAGB
d_13ens_1NAGNAGB
d_14ens_1NAGNAGB
d_15ens_1NAGNAGB
d_21ens_1THRASPA1 - 341
d_22ens_1NAGNAGA
d_23ens_1NAGNAGA
d_24ens_1NAGNAGA
d_25ens_1NAGNAGA
d_31ens_1THRASPC1 - 341
d_32ens_1NAGNAGC
d_33ens_1NAGNAGC
d_34ens_1NAGNAGC
d_35ens_1NAGNAGC
d_11ens_2GLNPROF1 - 215
d_21ens_2GLNPROE1 - 215
d_31ens_2GLNPROD1 - 215
d_11ens_3ASPCYSH1 - 218
d_21ens_3ASPCYSG1 - 218
d_31ens_3ASPCYSI1 - 218

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Protein Hemagglutinin


Mass: 58608.316 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#2: Antibody ab109 Fab heavy chain


Mass: 23267.232 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody ab109 Fab light chain


Mass: 23806.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 6 / 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

Component
IDNameTypeEntity IDParent-IDSource
1hemagglutinin H1 Solomon Islands/03/2006 in complex with ab109 FabCOMPLEX#1-#30RECOMBINANT
2HemagglutininCOMPLEX#11RECOMBINANT
3ab109 Fab heavy chain, ab 109 Fab light chainCOMPLEX#2-#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Influenza A virus (A/Solomon Islands/3/2006(H1N1))464623
23Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
23Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 1.07 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.8.6image acquisition
13RELION3.1.23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67533 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 70.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01418588
ELECTRON MICROSCOPYf_angle_d0.79425284
ELECTRON MICROSCOPYf_dihedral_angle_d8.7542577
ELECTRON MICROSCOPYf_chiral_restr0.0582829
ELECTRON MICROSCOPYf_plane_restr0.0053249
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000700445597514
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.000713573798389
ens_2d_2EELECTRON MICROSCOPYNCS constraints0.000703138039442
ens_2d_3DELECTRON MICROSCOPYNCS constraints0.000693235135163
ens_3d_2HELECTRON MICROSCOPYNCS constraints0.00069628728788
ens_3d_3IELECTRON MICROSCOPYNCS constraints0.000703536899342

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