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- PDB-6whk: Minimally mutated anti-influenza broadly neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 6whk
TitleMinimally mutated anti-influenza broadly neutralizing antibody
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN/Immune System / antibody / influenza / hemagglutinin / IMMUNE SYSTEM / VIRAL PROTEIN-Immune System complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBajic, G. / Schmidt, A.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI89618-A1 United States
CitationJournal: To Be Published
Title: Minimally mutated anti-influenza broadly neutralizing antibody
Authors: Bajic, G. / Schmidt, A.G.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 1.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
C: Fab Heavy Chain
B: Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5595
Polymers74,7803
Non-polymers7792
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-29 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 76.330, 126.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules CB

#2: Antibody Fab Heavy Chain


Mass: 25869.141 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 Fab Light Chain


Mass: 22929.350 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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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Hemagglutinin HA1 chain


Mass: 25981.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Beijing/262/1995(H1N1))
Strain: A/Beijing/262/1995(H1N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7
#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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 83 molecules

#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→63.08 Å / Num. obs: 21307 / % possible obs: 100 % / Redundancy: 5.586 % / Biso Wilson estimate: 50.174 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.181 / Χ2: 1.058 / Net I/σ(I): 10.94 / Num. measured all: 119011 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.75.5791.5771.3512469223622350.4131.743100
2.7-2.85.7141.1012.0611063193719360.6581.21599.9
2.8-2.95.7180.8332.99560167316720.7860.9299.9
2.9-35.7350.633.98459147514750.870.696100
3-45.6460.20610.1144900795779530.9860.22899.9
4-55.5260.07620.8915861287028700.9950.084100
5-65.4070.07121.067045130313030.9960.079100
6-85.3460.06322.235613105010500.9970.07100
8-105.1980.0429.7419703803790.9980.04499.7
10-504.7890.03130.2920644324310.9990.03599.8
50-63.082.3330.0118.574310.01575

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HKX

4hkx


Resolution: 2.6→63.08 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2675 1057 4.96 %
Rwork0.2178 20246 -
obs0.2204 21303 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.87 Å2 / Biso mean: 53.4174 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 2.6→63.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 812 82 5835
Biso mean--69.4 41.22 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.720.40281170.343225162633
2.72-2.860.37581110.298424742585
2.86-3.040.33851350.270425092644
3.04-3.280.29711300.243524952625
3.28-3.60.25711430.21725012644
3.61-4.130.26271320.201125242656
4.13-5.20.21191360.171525542690
5.2-63.080.24861530.200426732826

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