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- PDB-6wf0: Crystal Structure of Broadly Neutralizing Antibody 3I14 Bound to ... -

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Basic information

Entry
Database: PDB / ID: 6wf0
TitleCrystal Structure of Broadly Neutralizing Antibody 3I14 Bound to the Influenza A H3 Hemagglutinin
Components
  • (Hemagglutinin) x 2
  • 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 / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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 / 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
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 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 1.2Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,83510
Polymers101,6404
Non-polymers3,1956
Water0
1
A: Hemagglutinin
B: Hemagglutinin
H: heavy chain
L: light chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)314,50430
Polymers304,91912
Non-polymers9,58518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area55940 Å2
ΔGint-76 kcal/mol
Surface area121670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.318, 130.318, 188.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 35232.695 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: A0A5P1MU07
#2: Protein Hemagglutinin /


Mass: 18920.895 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: A0A2P1E3C0

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Antibody , 2 types, 2 molecules HL

#3: Antibody heavy chain


Mass: 25125.328 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)

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Sugars , 2 types, 6 molecules

#5: 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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Rhap]{}}}}LINUCSPDB-CARE
#6: 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.: 2
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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Details

Has ligand of interestN

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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: 4.6 Å3/Da / Density % sol: 73.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18-24% w/v PEG 3350, 0.2M KCN, and 0.1M Bis-Tris-Propane pH7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 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: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.457→42.66 Å / Num. obs: 23612 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.09 / Rrim(I) all: 0.216 / Net I/σ(I): 8.92
Reflection shellResolution: 3.457→3.581 Å / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 2349 / CC1/2: 0.39 / Rpim(I) all: 0.459 / Rrim(I) all: 1.095 / % possible all: 98.7

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 405I

405i


Resolution: 3.46→42.66 Å / SU ML: 0.4124 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7295
RfactorNum. reflection% reflection
Rfree0.2819 1989 8.43 %
Rwork0.231 --
obs0.2353 23583 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.46→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 211 0 7170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327325
X-RAY DIFFRACTIONf_angle_d0.65259944
X-RAY DIFFRACTIONf_chiral_restr0.05051146
X-RAY DIFFRACTIONf_plane_restr0.00471269
X-RAY DIFFRACTIONf_dihedral_angle_d10.9941090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.46-3.540.38181360.33741529X-RAY DIFFRACTION97.2
3.54-3.640.32721440.27991551X-RAY DIFFRACTION99.82
3.64-3.740.30831460.2691539X-RAY DIFFRACTION99.88
3.75-3.870.32921360.25331544X-RAY DIFFRACTION99.59
3.87-40.29711460.26151516X-RAY DIFFRACTION99.46
4-4.160.30031440.24261546X-RAY DIFFRACTION99.53
4.16-4.350.31681460.22431563X-RAY DIFFRACTION99.71
4.35-4.580.25191420.21021532X-RAY DIFFRACTION99.7
4.58-4.870.29061430.19131558X-RAY DIFFRACTION99.47
4.87-5.240.28381390.19921544X-RAY DIFFRACTION99.23
5.24-5.770.26251400.20111541X-RAY DIFFRACTION99.59
5.77-6.60.2531380.22431544X-RAY DIFFRACTION99
6.6-8.310.26781480.24451546X-RAY DIFFRACTION98.83
8.31-42.660.2491410.22171541X-RAY DIFFRACTION96.72

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