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- PDB-8u44: CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8u44
TitleCryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06
Components
  • 05.GC.w2.3C10-H1_SI06 Heavy chain
  • 05.GC.w2.3C10-H1_SI06 Light chain
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza virus / hemagglutinin / H1 / monoclonal antibody / virus / 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 speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsMoore, N. / Han, J. / Ward, A.B. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J Exp Med / Year: 2024
Title: Maturation of germinal center B cells after influenza virus vaccination in humans.
Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron ...Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron J Schmitz / Kenneth B Hoehn / Juan Manuel Carreño / Temima Yellin / Teresa Suessen / William D Middleton / Sharlene A Teefey / Rachel M Presti / Florian Krammer / Jackson S Turner / Andrew B Ward / Ian A Wilson / Steven H Kleinstein / Ali H Ellebedy /
Abstract: Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation ...Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.
History
DepositionSep 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: 05.GC.w2.3C10-H1_SI06 Heavy chain
X: 05.GC.w2.3C10-H1_SI06 Light chain
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
S: 05.GC.w2.3C10-H1_SI06 Heavy chain
T: 05.GC.w2.3C10-H1_SI06 Light chain
G: Hemagglutinin HA1 chain
I: Hemagglutinin HA2 chain
U: 05.GC.w2.3C10-H1_SI06 Heavy chain
W: 05.GC.w2.3C10-H1_SI06 Light chain
H: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,89821
Polymers357,90712
Non-polymers1,9919
Water00
1


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

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Components

#1: Protein 05.GC.w2.3C10-H1_SI06 Heavy chain


Mass: 25771.057 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 05.GC.w2.3C10-H1_SI06 Light chain


Mass: 25706.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Hemagglutinin HA1 chain


Mass: 40835.902 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#4: Protein Hemagglutinin HA2 chain


Mass: 26988.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A7Y8I1
#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.: 9 / 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
1Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10COMPLEX#3-#4, #1-#20RECOMBINANT
2FabCOMPLEX#1-#21RECOMBINANT
3HACOMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
32Cricetulus griseus (Chinese hamster)10029
43Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 7.6 / Details: Tris-buffered saline
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 25 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 / Nominal magnification: 29000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv3particle selection
2Leginonimage acquisition
4cryoSPARCv3CTF correction
8PHENIXmodel refinement
10cryoSPARCv3initial Euler assignment
11cryoSPARCv3final Euler assignment
13cryoSPARCv33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00617298
ELECTRON MICROSCOPYf_angle_d0.99223434
ELECTRON MICROSCOPYf_dihedral_angle_d4.6062348
ELECTRON MICROSCOPYf_chiral_restr0.0562528
ELECTRON MICROSCOPYf_plane_restr0.0063047

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