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- PDB-9ds1: Crystal structure of 241_2F04 Fab in complex with H1 HA from A/Ca... -

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Basic information

Entry
Database: PDB / ID: 9ds1
TitleCrystal structure of 241_2F04 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Components
  • (Hemagglutinin ...) x 2
  • 241_2F04, Heavy chain
  • 241_2F04, Light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H1N1 / Antibody / Hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
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: 2.4 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: Hemagglutinin HA1 chai
B: Hemagglutinin HA2 chain
H: 241_2F04, Heavy chain
L: 241_2F04, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6766
Polymers103,8684
Non-polymers8082
Water2,324129
1
A: Hemagglutinin HA1 chai
B: Hemagglutinin HA2 chain
H: 241_2F04, Heavy chain
L: 241_2F04, Light chain
hetero molecules

A: Hemagglutinin HA1 chai
B: Hemagglutinin HA2 chain
H: 241_2F04, Heavy chain
L: 241_2F04, Light chain
hetero molecules

A: Hemagglutinin HA1 chai
B: Hemagglutinin HA2 chain
H: 241_2F04, Heavy chain
L: 241_2F04, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,02818
Polymers311,60512
Non-polymers2,4236
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Buried area46990 Å2
ΔGint-220 kcal/mol
Surface area119410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.466, 129.466, 443.769
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-215-

HOH

21B-238-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chai


Mass: 36213.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A5B9ZSV0
#2: Protein Hemagglutinin HA2 chain


Mass: 19992.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6J3XB93

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Antibody , 2 types, 2 molecules HL

#3: Antibody 241_2F04, Heavy chain


Mass: 24169.281 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 241_2F04, Light chain


Mass: 23493.066 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)

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Sugars , 2 types, 2 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.: 1
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: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Non-polymers , 1 types, 129 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, pH 6.4, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→39.43 Å / Num. obs: 54268 / % possible obs: 96 % / Redundancy: 19 % / CC1/2: 1 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.04 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 54123 / CC1/2: 0.9 / Rpim(I) all: 0.28

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5127: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.43 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2633 2768 5.11 %
Rwork0.2201 --
obs0.2222 54191 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7297 0 53 129 7479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037521
X-RAY DIFFRACTIONf_angle_d0.64410208
X-RAY DIFFRACTIONf_dihedral_angle_d17.7962705
X-RAY DIFFRACTIONf_chiral_restr0.0451132
X-RAY DIFFRACTIONf_plane_restr0.0051311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.46651360.38272362X-RAY DIFFRACTION90
2.44-2.480.35531270.34452402X-RAY DIFFRACTION91
2.48-2.530.37981250.322383X-RAY DIFFRACTION90
2.53-2.580.32811290.29972438X-RAY DIFFRACTION92
2.58-2.640.32681550.2862437X-RAY DIFFRACTION92
2.64-2.70.28881490.26692441X-RAY DIFFRACTION93
2.7-2.770.32811060.26892530X-RAY DIFFRACTION94
2.77-2.840.34661270.25912506X-RAY DIFFRACTION94
2.84-2.930.35091460.2672537X-RAY DIFFRACTION95
2.93-3.020.30761360.25732564X-RAY DIFFRACTION96
3.02-3.130.26221420.2522580X-RAY DIFFRACTION97
3.13-3.260.3131420.24452602X-RAY DIFFRACTION97
3.26-3.40.26411540.2322626X-RAY DIFFRACTION98
3.4-3.580.28691460.232638X-RAY DIFFRACTION99
3.58-3.810.25091330.22192687X-RAY DIFFRACTION99
3.81-4.10.26551280.19232676X-RAY DIFFRACTION99
4.1-4.510.22441620.17052689X-RAY DIFFRACTION100
4.51-5.160.18981360.17272725X-RAY DIFFRACTION100
5.16-6.50.20291480.1942738X-RAY DIFFRACTION99
6.5-39.430.2321410.18742862X-RAY DIFFRACTION99

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