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- PDB-9mev: Structure of H1H3:FluA20 Chimeric Antigen Complex -

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Basic information

Entry
Database: PDB / ID: 9mev
TitleStructure of H1H3:FluA20 Chimeric Antigen Complex
Components
  • FluA20 Heavy Chain Fab
  • FluA20 Light Chain Fab
  • H1H3 HA
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / HA / Hemagglutinin / Antigen / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSeraj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Biorxiv / Year: 2025
Title: Structure-based Design of Chimeric Influenza Hemagglutinins to Elicit Cross-group Immunity.
Authors: Castro, K.M. / Ayardulabi, R. / Wehrle, S. / Cui, H. / Georgeon, S. / Schmidt, J. / Xiao, S. / Seraj, N. / Harshbarger, W. / Mallett, C.P. / Vassilev, V. / Saelens, X. / Correia, B.E.
History
DepositionDec 8, 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

Downloads & links

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Assembly

Deposited unit
B: H1H3 HA
H: FluA20 Heavy Chain Fab
L: FluA20 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,41811
Polymers74,4003
Non-polymers1,0188
Water10,611589
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.641, 93.465, 86.434
Angle α, β, γ (deg.)90.000, 93.482, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules B

#1: Protein H1H3 HA


Mass: 25737.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Homo sapiens (human)

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Antibody , 2 types, 2 molecules HL

#2: Antibody FluA20 Heavy Chain Fab


Mass: 25154.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody FluA20 Light Chain Fab


Mass: 23508.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 2 molecules

#4: 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.: 1
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
#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.: 1 / 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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Non-polymers , 2 types, 595 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M PCB, pH 6, 25% w/v PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→44.82 Å / Num. obs: 45825 / % possible obs: 92.14 % / Redundancy: 3 % / Biso Wilson estimate: 24.98 Å2 / CC1/2: 0.987 / Rrim(I) all: 0.067 / Net I/σ(I): 17.9
Reflection shellResolution: 2.06→2.09 Å / Num. unique obs: 945 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→44.82 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.4274
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 3152 4.39 %
Rwork0.1809 68608 -
obs0.1821 45825 72.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.11 Å2
Refinement stepCycle: LAST / Resolution: 2.06→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 65 589 5699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01085270
X-RAY DIFFRACTIONf_angle_d1.29027174
X-RAY DIFFRACTIONf_chiral_restr0.0708801
X-RAY DIFFRACTIONf_plane_restr0.0056919
X-RAY DIFFRACTIONf_dihedral_angle_d14.1011962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.3444450.3106905X-RAY DIFFRACTION22.11
2.09-2.120.328560.29931242X-RAY DIFFRACTION30.17
2.12-2.150.3226700.27331457X-RAY DIFFRACTION36.01
2.15-2.190.2611690.25461722X-RAY DIFFRACTION42.17
2.19-2.230.2646880.2421989X-RAY DIFFRACTION48.11
2.23-2.270.24751000.22912157X-RAY DIFFRACTION52.42
2.27-2.320.2586990.22132265X-RAY DIFFRACTION55.29
2.32-2.370.23291200.21132318X-RAY DIFFRACTION57.46
2.37-2.430.25181130.20422571X-RAY DIFFRACTION62.93
2.43-2.490.23271300.20262725X-RAY DIFFRACTION66.86
2.49-2.550.2181390.20312941X-RAY DIFFRACTION71.35
2.55-2.630.24691250.19973158X-RAY DIFFRACTION77.08
2.63-2.710.19961790.20033570X-RAY DIFFRACTION87.68
2.71-2.810.21531650.20273852X-RAY DIFFRACTION92.75
2.81-2.920.21741860.19183831X-RAY DIFFRACTION95.3
2.92-3.060.22311800.18913986X-RAY DIFFRACTION97.38
3.06-3.220.25211760.17894091X-RAY DIFFRACTION98.36
3.22-3.420.23671810.17163960X-RAY DIFFRACTION98.08
3.42-3.680.18151900.16473907X-RAY DIFFRACTION95.66
3.68-4.050.18891790.15653946X-RAY DIFFRACTION95.86
4.05-4.640.15711900.14264066X-RAY DIFFRACTION99.02
4.64-5.840.15251860.15864029X-RAY DIFFRACTION99.13
5.84-44.820.23481860.18733920X-RAY DIFFRACTION95.71

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