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- PDB-9azt: CH67 Fab bound to A/Massachusetts/1/1990 influenza hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 9azt
TitleCH67 Fab bound to A/Massachusetts/1/1990 influenza hemagglutinin head with a G189E mutation (1)
Components
  • CH67 Fab heavy chain
  • CH67 Fab light chain
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / influenza / hemagglutinin / UCA / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / 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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsMaurer, D.P. / Schmidt, A.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI146779 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
CitationJournal: Immunity / Year: 2025
Title: Antigenic drift expands influenza viral escape pathways from recalled humoral immunity.
Authors: Maurer, D.P. / Vu, M. / Schmidt, A.G.
History
DepositionMar 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Hemagglutinin HA1 chain
H: CH67 Fab heavy chain
L: CH67 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9245
Polymers75,2793
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.752, 91.700, 110.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Hemagglutinin HA1 chain


Mass: 25462.266 Da / Num. of mol.: 1 / Fragment: head domain / Mutation: G189E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Massachusetts/1/1990(H1N1) / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q07775
#2: Antibody CH67 Fab heavy chain


Mass: 26988.180 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 CH67 Fab light chain


Mass: 22828.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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: isolated from a genetically manipulated source
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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8K, 100 mM HEPES, pH 7, 500 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.94→47.2 Å / Num. obs: 17764 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 107.88 Å2 / CC1/2: 1 / Net I/σ(I): 22.92
Reflection shellResolution: 2.94→3.12 Å / Num. unique obs: 2695 / CC1/2: 0.932

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.94→47.2 Å / SU ML: 0.5682 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 40.9607
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3384 1774 10 %
Rwork0.294 15972 -
obs0.2986 17746 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 139.78 Å2
Refinement stepCycle: LAST / Resolution: 2.94→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 42 0 4977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385111
X-RAY DIFFRACTIONf_angle_d0.75486973
X-RAY DIFFRACTIONf_chiral_restr0.0464774
X-RAY DIFFRACTIONf_plane_restr0.0074891
X-RAY DIFFRACTIONf_dihedral_angle_d5.0692708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.020.52891200.49581073X-RAY DIFFRACTION89.3
3.02-3.110.43981350.41531228X-RAY DIFFRACTION99.78
3.11-3.210.43981350.38351216X-RAY DIFFRACTION99.78
3.21-3.330.42131360.38591213X-RAY DIFFRACTION99.85
3.33-3.460.44821340.37621217X-RAY DIFFRACTION99.7
3.46-3.620.48031360.35781221X-RAY DIFFRACTION99.93
3.62-3.810.42461370.34491238X-RAY DIFFRACTION100
3.81-4.050.32381360.32321219X-RAY DIFFRACTION100
4.05-4.360.33751380.31241247X-RAY DIFFRACTION99.93
4.36-4.80.32991380.26711235X-RAY DIFFRACTION99.93
4.8-5.490.26611390.261252X-RAY DIFFRACTION99.93
5.49-6.910.31141410.28181269X-RAY DIFFRACTION99.93
6.92-47.20.31041490.24531344X-RAY DIFFRACTION99.8

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