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- PDB-8txt: Crystal structure of 05.GC.w13.02 Fab in complex with H5 HA from ... -

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Basic information

Entry
Database: PDB / ID: 8txt
TitleCrystal structure of 05.GC.w13.02 Fab in complex with H5 HA from A/Viet Nam/1203/2004(H5N1)
Components
  • (Hemagglutinin) x 2
  • GC_W13B_B, Fab heavy chain
  • GC_w13_B, Fab 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 / 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: 3.19 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 13, 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
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
H: GC_W13B_B, Fab heavy chain
L: GC_w13_B, Fab light chain
G: GC_W13B_B, Fab heavy chain
I: GC_w13_B, Fab light chain
J: GC_W13B_B, Fab heavy chain
K: GC_w13_B, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,47025
Polymers316,05112
Non-polymers4,41913
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52880 Å2
ΔGint-184 kcal/mol
Surface area112450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.461, 232.604, 233.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin


Mass: 37948.020 Da / Num. of mol.: 3 / Fragment: HA1 subdomain (UNP residues 17-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31
#2: Protein Hemagglutinin


Mass: 20414.504 Da / Num. of mol.: 3 / Fragment: HA2 subdomain (UNP residues 330-503)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/Viet Nam/1203/2004(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6B7HQ27

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Antibody , 2 types, 6 molecules HGJLIK

#3: Antibody GC_W13B_B, Fab heavy chain


Mass: 23641.857 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)
#4: Antibody GC_w13_B, Fab light chain


Mass: 23345.848 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)

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Sugars , 3 types, 13 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 4
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
#7: 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.: 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

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Details

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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium sulfate, pH 6.2, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.19→47.12 Å / Num. obs: 57122 / % possible obs: 96.6 % / Redundancy: 5.8 % / CC1/2: 0.976 / Rpim(I) all: 0.096 / Rsym value: 0.129 / Net I/σ(I): 7.8
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 689 / CC1/2: 0.36 / Rpim(I) all: 0.8 / Rsym value: 1

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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 4FQI

4fqi


Resolution: 3.19→47.12 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 2891 5.06 %
Rwork0.2174 --
obs0.2196 57110 79.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21813 0 288 0 22101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222641
X-RAY DIFFRACTIONf_angle_d0.48430713
X-RAY DIFFRACTIONf_dihedral_angle_d5.4313163
X-RAY DIFFRACTIONf_chiral_restr0.0483433
X-RAY DIFFRACTIONf_plane_restr0.0043954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.240.204360.3078144X-RAY DIFFRACTION4
3.25-3.30.4546210.3035440X-RAY DIFFRACTION14
3.3-3.360.3705510.29021131X-RAY DIFFRACTION35
3.36-3.430.3122870.28061748X-RAY DIFFRACTION54
3.43-3.50.30911200.28112126X-RAY DIFFRACTION66
3.5-3.570.31971330.26022453X-RAY DIFFRACTION76
3.57-3.650.29571310.25722709X-RAY DIFFRACTION83
3.65-3.750.34271400.26142848X-RAY DIFFRACTION88
3.75-3.850.30671520.25522967X-RAY DIFFRACTION92
3.85-3.960.30641730.25143061X-RAY DIFFRACTION94
3.96-4.090.28931670.22593096X-RAY DIFFRACTION95
4.09-4.230.2621500.2123067X-RAY DIFFRACTION94
4.23-4.40.25621670.19893177X-RAY DIFFRACTION97
4.4-4.60.20981810.19583146X-RAY DIFFRACTION97
4.6-4.850.23671660.19863201X-RAY DIFFRACTION97
4.85-5.150.25891800.18983127X-RAY DIFFRACTION97
5.15-5.550.26221480.19453184X-RAY DIFFRACTION96
5.55-6.10.24931640.20913134X-RAY DIFFRACTION95
6.1-6.980.24171680.21783090X-RAY DIFFRACTION94
6.98-8.790.22862150.19323155X-RAY DIFFRACTION96
8.79-47.120.20471710.19593215X-RAY DIFFRACTION93

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