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- PDB-6wex: Crystal Structure of Broadly Neutralizing Antibody 3I14-D93N Muta... -

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Basic information

Entry
Database: PDB / ID: 6wex
TitleCrystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant Bound to the Influenza A H6 Hemagglutinin
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
  • heavy chain
  • light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Influenza / Hemagglutinin / Stem epitope / VIRAL 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 / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex ...Haemagglutinin, influenzavirus B / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / 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
Hemagglutinin HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsHarshbarger, W.D. / Lockbaum, G.J. / Deming, D.T. / Attatippaholkun, N. / Schiffer, C.A. / Marasco, W.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI121285 United States
Department of Defense (DOD, United States)W81XWH-15-1-0317 United States
CitationJournal: Nat Commun / Year: 2021
Title: Unique structural solution from a V H 3-30 antibody targeting the hemagglutinin stem of influenza A viruses.
Authors: Harshbarger, W.D. / Deming, D. / Lockbaum, G.J. / Attatippaholkun, N. / Kamkaew, M. / Hou, S. / Somasundaran, M. / Wang, J.P. / Finberg, R.W. / Zhu, Q.K. / Schiffer, C.A. / Marasco, W.A.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 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

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Assembly

Deposited unit
E: Hemagglutinin
F: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2655
Polymers109,0444
Non-polymers2211
Water00
1
E: Hemagglutinin
F: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules

E: Hemagglutinin
F: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules

E: Hemagglutinin
F: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)327,79615
Polymers327,13212
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area48490 Å2
ΔGint-248 kcal/mol
Surface area116420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.810, 117.810, 438.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Hemagglutinin


Mass: 36487.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0M3KL64
#2: Protein Hemagglutinin HA2 chain


Mass: 25056.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X245
#3: Antibody heavy chain


Mass: 25140.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Antibody light chain


Mass: 22359.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MIB Buffer (sodium malonate, imidazole, and boric acid in the molar ratios 2:3:3) pH 5.0, and 25% PEG 1500

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.49→48.26 Å / Num. obs: 15294 / % possible obs: 99.3 % / Redundancy: 9.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.058 / Net I/σ(I): 9.89
Reflection shellResolution: 3.49→3.615 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 3.15 / Num. unique obs: 1421 / CC1/2: 0.86 / Rpim(I) all: 0.219 / Rrim(I) all: 0.686 / % possible all: 94.5

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XKD

4xkd


Resolution: 3.49→48.26 Å / SU ML: 0.6936 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.513
RfactorNum. reflection% reflectionSelection details
Rfree0.3327 1530 10.01 %random
Rwork0.2758 ---
obs0.2814 15291 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.49→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7109 0 14 0 7123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237289
X-RAY DIFFRACTIONf_angle_d0.6099898
X-RAY DIFFRACTIONf_chiral_restr0.04351089
X-RAY DIFFRACTIONf_plane_restr0.00371276
X-RAY DIFFRACTIONf_dihedral_angle_d13.64771004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.60.4681280.37581152X-RAY DIFFRACTION93.98
3.6-3.730.42131370.3571235X-RAY DIFFRACTION99.93
3.73-3.880.44011380.33731236X-RAY DIFFRACTION100
3.88-4.060.33871390.29861249X-RAY DIFFRACTION99.86
4.06-4.270.35611360.27721236X-RAY DIFFRACTION99.93
4.27-4.540.30071400.25541257X-RAY DIFFRACTION100
4.54-4.890.31931400.25151249X-RAY DIFFRACTION99.78
4.89-5.380.32881390.26131252X-RAY DIFFRACTION99.86
5.38-6.160.31631390.27411257X-RAY DIFFRACTION100
6.16-7.750.34271430.27891283X-RAY DIFFRACTION100
7.75-48.260.27851510.24351355X-RAY DIFFRACTION99.74

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