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- PDB-8ty7: Crystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from... -

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Basic information

Entry
Database: PDB / ID: 8ty7
TitleCrystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Components
  • (Hemagglutinin) x 2
  • GC_w2_3C10, heavy chain
  • GC_w2_3C10, light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H1N1 / Antibody / Hemagglutinin / 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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsLin, T.H. / Moore, N. / 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
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
H: GC_w2_3C10, heavy chain
L: GC_w2_3C10, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4527
Polymers103,7884
Non-polymers6643
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: GC_w2_3C10, heavy chain
L: GC_w2_3C10, light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w2_3C10, heavy chain
L: GC_w2_3C10, light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w2_3C10, heavy chain
L: GC_w2_3C10, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,35521
Polymers311,36412
Non-polymers1,9919
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area50320 Å2
ΔGint-259 kcal/mol
Surface area114580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.006, 201.006, 201.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Hemagglutinin


Mass: 36672.352 Da / Num. of mol.: 1 / Fragment: HA1 subdomain (UNP residues 18-344)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G8EHJ9
#2: Protein Hemagglutinin


Mass: 20206.320 Da / Num. of mol.: 1 / Fragment: HA2 subdomain (UNP residues 326-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I1ZFF9
#3: Protein GC_w2_3C10, heavy chain


Mass: 23544.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody GC_w2_3C10, light chain


Mass: 23364.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#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.: 3 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, pH 6.4, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.21→41.9 Å / Num. obs: 22209 / % possible obs: 100 % / Redundancy: 22.1 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rsym value: 0.196 / Net I/σ(I): 22
Reflection shellResolution: 3.21→3.26 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2179 / CC1/2: 0.23 / Rsym value: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M4Y

4m4y


Resolution: 3.21→41.03 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 1171 5.27 %
Rwork0.2445 --
obs0.247 22209 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.21→41.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 42 0 7219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027381
X-RAY DIFFRACTIONf_angle_d0.43810019
X-RAY DIFFRACTIONf_dihedral_angle_d3.9141014
X-RAY DIFFRACTIONf_chiral_restr0.0491121
X-RAY DIFFRACTIONf_plane_restr0.0041286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.350.40481510.34052603X-RAY DIFFRACTION100
3.36-3.530.38571390.31092601X-RAY DIFFRACTION100
3.53-3.750.31511040.2892646X-RAY DIFFRACTION100
3.75-4.040.29551440.25022623X-RAY DIFFRACTION100
4.04-4.450.32291610.27722601X-RAY DIFFRACTION100
4.45-5.090.2851540.24332614X-RAY DIFFRACTION100
5.1-6.410.30391390.25942658X-RAY DIFFRACTION100
6.41-41.030.25751790.20682692X-RAY DIFFRACTION100

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