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- PDB-9dsc: Crystal structure of Apo-241_2F04-A95a mutant Fab -

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Basic information

Entry
Database: PDB / ID: 9dsc
TitleCrystal structure of Apo-241_2F04-A95a mutant Fab
Components
  • 241_2F04-A95a, Heavy chain
  • 241_2F04-A95a, Light chain
KeywordsIMMUNE SYSTEM / Antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLin, T.H. / 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: Nat Commun / Year: 2025
Title: Structurally convergent antibodies derived from different vaccine strategies target the influenza virus HA anchor epitope with a subset of V3 and V3 genes.
Authors: Ting-Hui Lin / Chang-Chun David Lee / Monica L Fernández-Quintero / James A Ferguson / Julianna Han / Xueyong Zhu / Wenli Yu / Jenna J Guthmiller / Florian Krammer / Patrick C Wilson / ...Authors: Ting-Hui Lin / Chang-Chun David Lee / Monica L Fernández-Quintero / James A Ferguson / Julianna Han / Xueyong Zhu / Wenli Yu / Jenna J Guthmiller / Florian Krammer / Patrick C Wilson / Andrew B Ward / Ian A Wilson /
Abstract: H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine ...H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine to elicit broadly neutralizing antibodies (bnAbs). Identification and characterization of bnAbs elicited in natural infection and immunization to influenza virus hemagglutinin (HA) can provide insights for development of a universal influenza vaccine. Here, we structurally and biophysically characterize four antibodies that bind to a conserved region on the HA membrane-proximal region known as the anchor epitope. Despite some diversity in their V and V genes, the antibodies interact with the HA through germline-encoded residues in HCDR2 and LCDR3. Somatic mutations on HCDR3 also contribute hydrophobic interactions with the conserved HA epitope. This convergent binding mode provides extensive neutralization breadth against H1N1 viruses and suggests possible countermeasures against H1N1 viruses.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 241_2F04-A95a, Heavy chain
F: 241_2F04-A95a, Light chain
B: 241_2F04-A95a, Heavy chain
C: 241_2F04-A95a, Light chain


Theoretical massNumber of molelcules
Total (without water)95,1344
Polymers95,1344
Non-polymers00
Water12,052669
1
A: 241_2F04-A95a, Heavy chain
F: 241_2F04-A95a, Light chain


Theoretical massNumber of molelcules
Total (without water)47,5672
Polymers47,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
MethodPISA
2
B: 241_2F04-A95a, Heavy chain
C: 241_2F04-A95a, Light chain


Theoretical massNumber of molelcules
Total (without water)47,5672
Polymers47,5672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-25 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.254, 113.659, 160.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 241_2F04-A95a, Heavy chain


Mass: 24100.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 241_2F04-A95a, Light chain


Mass: 23467.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium acetate, pH 6.3, 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9183 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 76548 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 76269 / CC1/2: 0.4 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→46.41 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 3958 5.17 %
Rwork0.1996 --
obs0.2015 76548 96.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 0 669 7341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026824
X-RAY DIFFRACTIONf_angle_d0.599278
X-RAY DIFFRACTIONf_dihedral_angle_d5.633944
X-RAY DIFFRACTIONf_chiral_restr0.0431046
X-RAY DIFFRACTIONf_plane_restr0.0041186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.36981020.34282177X-RAY DIFFRACTION81
2.03-2.060.35851350.33282438X-RAY DIFFRACTION92
2.06-2.080.31291350.30622417X-RAY DIFFRACTION91
2.08-2.110.32871430.28662423X-RAY DIFFRACTION92
2.11-2.140.29161270.26782556X-RAY DIFFRACTION93
2.14-2.170.28221540.26292465X-RAY DIFFRACTION94
2.17-2.210.26321250.26462495X-RAY DIFFRACTION94
2.21-2.240.27661520.25242475X-RAY DIFFRACTION93
2.24-2.280.28871350.25042545X-RAY DIFFRACTION95
2.28-2.320.28841340.25412530X-RAY DIFFRACTION95
2.32-2.370.25561460.2542564X-RAY DIFFRACTION95
2.37-2.420.30321450.24312569X-RAY DIFFRACTION96
2.42-2.470.28511390.23792585X-RAY DIFFRACTION97
2.47-2.530.27371440.23182593X-RAY DIFFRACTION97
2.53-2.590.25831450.23162613X-RAY DIFFRACTION97
2.59-2.660.30341520.21872616X-RAY DIFFRACTION98
2.66-2.740.26141460.21512616X-RAY DIFFRACTION98
2.74-2.830.26171640.212631X-RAY DIFFRACTION98
2.83-2.930.27291380.2172670X-RAY DIFFRACTION98
2.93-3.040.28861300.21682685X-RAY DIFFRACTION99
3.04-3.180.25891310.21312689X-RAY DIFFRACTION99
3.18-3.350.22771320.2042706X-RAY DIFFRACTION99
3.35-3.560.22431590.18722696X-RAY DIFFRACTION100
3.56-3.830.24581340.18842728X-RAY DIFFRACTION100
3.84-4.220.19831670.16582719X-RAY DIFFRACTION100
4.22-4.830.1771580.1352736X-RAY DIFFRACTION100
4.83-6.080.18231490.14532777X-RAY DIFFRACTION100
6.08-46.410.17061370.17132876X-RAY DIFFRACTION98

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