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

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Basic information

Entry
Database: PDB / ID: 7kqh
TitleAntibodies that engage the hemagglutinin receptor-binding site of influenza B viruses
Components
  • 2365 Fab heavy chain
  • 2365 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 / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Haemagglutinin, influenzavirus B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 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 23, 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: Hemagglutinin
H: 2365 Fab heavy chain
L: 2365 Fab light chain
C: 2365 Fab heavy chain
D: 2365 Fab light chain
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,6828
Polymers164,3476
Non-polymers1,3352
Water00
1
A: Hemagglutinin
C: 2365 Fab heavy chain
D: 2365 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7604
Polymers82,1733
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-19 kcal/mol
Surface area30410 Å2
MethodPISA
2
H: 2365 Fab heavy chain
L: 2365 Fab light chain
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9224
Polymers82,1733
Non-polymers7491
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-16 kcal/mol
Surface area31160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.660, 132.660, 93.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Hemagglutinin


Mass: 32674.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Phuket/3073/2013 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A4P8YRB6
#2: Antibody 2365 Fab heavy chain


Mass: 25880.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 2365 Fab light chain


Mass: 23618.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES pH 7.5, 25% (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 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→114.89 Å / Num. obs: 23115 / % possible obs: 99.9 % / Redundancy: 6.288 % / Biso Wilson estimate: 143.497 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.253 / Rrim(I) all: 0.276 / Χ2: 1.001 / Net I/σ(I): 5.3 / Num. measured all: 145358
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
3.5-3.66.1446.6020.2511656190118977.21899.8
3.6-3.76.1845.8670.310358167516756.4141000.114
3.7-3.85.7193.0680.518527149314913.38399.90.182
3.8-3.96.6482.2410.789055136213622.4331000.312
3.9-46.6981.511.168171122012201.6371000.577
4-66.3670.4634.816935710896108930.5051000.949
6-106.1990.1312.7522250359135890.14299.90.994
10-205.9910.06720.0451708658630.07399.80.996
20-506.4750.0621.887641181180.0661000.998
50-114.897.1430.0724.0550770.0761000.998

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4fqj

4fql


Resolution: 3.5→114.89 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 42.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3002 977 4.24 %
Rwork0.2522 22069 -
obs0.2546 23046 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 294.37 Å2 / Biso mean: 180.4945 Å2 / Biso min: 85.89 Å2
Refinement stepCycle: final / Resolution: 3.5→114.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10182 0 89 0 10271
Biso mean--245.28 --
Num. residues----1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410496
X-RAY DIFFRACTIONf_angle_d0.70914261
X-RAY DIFFRACTIONf_dihedral_angle_d13.7453838
X-RAY DIFFRACTIONf_chiral_restr0.0471618
X-RAY DIFFRACTIONf_plane_restr0.0041832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.680.48471240.46883156328098
3.68-3.920.41751180.378431333251100
3.92-4.220.3981700.346331323302100
4.22-4.640.39541480.284931693317100
4.64-5.310.34271360.253531583294100
5.31-6.690.3611480.253731613309100
6.7-114.890.18461330.188431603293100

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