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- PDB-6wf1: Crystal Structure of Broadly Neutralizing Antibody 3I14 Bound to ... -

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Basic information

Entry
Database: PDB / ID: 6wf1
TitleCrystal Structure of Broadly Neutralizing Antibody 3I14 Bound to the Influenza A H10 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


viral budding from plasma membrane / 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 / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin HA2 chain
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.19 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 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
B: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7945
Polymers107,5734
Non-polymers2211
Water00
1
A: Hemagglutinin
B: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin HA2 chain
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,38315
Polymers322,71912
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area47090 Å2
ΔGint-254 kcal/mol
Surface area115800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.021, 127.021, 158.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
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

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Components

#1: Protein Hemagglutinin


Mass: 35398.980 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: A0A0J9X252, UniProt: A0A059T4A1*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 25093.582 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: A0A0J9X253, UniProt: A0A059T4A1*PLUS
#3: Antibody heavy chain


Mass: 24719.873 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: 22360.723 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: 3.67 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 15% w/v PEG 4000, 0.15M Ammonium Sulfate, 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 4.19→41.58 Å / Num. obs: 9561 / % possible obs: 84.5 % / Redundancy: 3.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.063 / Rrim(I) all: 0.127 / Net I/σ(I): 8.8
Reflection shellResolution: 4.19→4.41 Å / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 775 / CC1/2: 0.646 / Rpim(I) all: 0.406 / Rrim(I) all: 0.715

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TGV

5tgv


Resolution: 4.19→41.58 Å / SU ML: 0.5766 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.8662
RfactorNum. reflection% reflection
Rfree0.3085 961 10.05 %
Rwork0.2607 --
obs0.2656 9558 84.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.19→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 14 0 6973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00187122
X-RAY DIFFRACTIONf_angle_d0.47849663
X-RAY DIFFRACTIONf_chiral_restr0.04041073
X-RAY DIFFRACTIONf_plane_restr0.00381255
X-RAY DIFFRACTIONf_dihedral_angle_d13.77152539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.19-4.410.34151090.33771008X-RAY DIFFRACTION70.03
4.41-4.690.32861160.27361059X-RAY DIFFRACTION74.56
4.69-5.050.3391380.28021186X-RAY DIFFRACTION83.74
5.05-5.550.29931490.27121304X-RAY DIFFRACTION91.5
5.56-6.350.33271540.28571342X-RAY DIFFRACTION92.57
6.36-7.990.32631500.2941343X-RAY DIFFRACTION92.1
8-41.580.28391450.22531355X-RAY DIFFRACTION87.46

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