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- PDB-7kqi: Antibodies that engage the hemagglutinin receptor-binding site of... -

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Basic information

Entry
Database: PDB / ID: 7kqi
TitleAntibodies that engage the hemagglutinin receptor-binding site of influenza B viruses
Components
  • 1209 Fab heavy chain
  • 1209 Fab light chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / influenza / antibody / receptor binding site / vaccine / B cell / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


viral budding from plasma membrane / host cell surface receptor binding / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane ...viral budding from plasma membrane / host cell surface receptor binding / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / 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 speciesHomo sapiens (human)
Influenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsBajic, G. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI089618 United States
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Antibodies That Engage the Hemagglutinin Receptor-Binding Site of Influenza B Viruses.
Authors: Bajic, G. / Harrison, S.C.
History
DepositionNov 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 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

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Assembly

Deposited unit
A: 1209 Fab heavy chain
C: 1209 Fab light chain
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2655
Polymers82,0923
Non-polymers1,1732
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-15 kcal/mol
Surface area29990 Å2
Unit cell
Length a, b, c (Å)128.100, 128.100, 235.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody 1209 Fab heavy chain


Mass: 25961.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 1209 Fab light chain


Mass: 23552.197 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: Protein Hemagglutinin


Mass: 32578.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Yamagata/16/1988 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A4D5Q0, UniProt: P18880*PLUS
#4: 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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-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
DManpb1-4DGlcpNAcb1-6DGlcpNAcb1-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/a6-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200 mM sodium citrate pH 7.0, 20% (wt/vol) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.2→49.61 Å / Num. obs: 8864 / % possible obs: 99.8 % / Redundancy: 20.598 % / Biso Wilson estimate: 183.899 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.74 / Rrim(I) all: 0.76 / Χ2: 0.711 / Net I/σ(I): 3.51 / Num. measured all: 182579 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.2-4.522.5956.6480.6115970.246.8100
4.5-521.7753.7581.0618980.3263.84799.9
5-620.6182.4991.5521960.4142.562100
6-1020.1620.6245.7424300.9880.64299.9
10-2015.0090.1614.46400.9930.16699.4
20-3013.1050.12315.18760.9960.128100
30-4011.350.10415.02200.9990.10995.2
40-509.4290.09415.5870.9990.098100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQJ, 4FQL

4fqj

4fql


Resolution: 4.2→49.61 Å / SU ML: 0.99 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 51.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4203 851 9.6 %
Rwork0.3721 8010 -
obs0.3769 8861 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 435.96 Å2 / Biso mean: 234.9994 Å2 / Biso min: 151.3 Å2
Refinement stepCycle: final / Resolution: 4.2→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4992 0 78 0 5070
Biso mean--271.07 --
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055183
X-RAY DIFFRACTIONf_angle_d0.8677039
X-RAY DIFFRACTIONf_dihedral_angle_d10.688745
X-RAY DIFFRACTIONf_chiral_restr0.056806
X-RAY DIFFRACTIONf_plane_restr0.006897
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.2-4.460.43151240.390213051429100
4.46-4.810.41061470.404212841431100
4.81-5.290.42281610.379912921453100
5.29-6.050.4331340.394213241458100
6.06-7.620.4181400.413613511491100
7.63-49.610.41861450.34761454159999

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