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

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Basic information

Entry
Database: PDB / ID: 6wez
TitleCrystal Structure of Broadly Neutralizing Antibody 3I14-D93N Mutant 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 / 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 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 / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 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
Revision 1.3Nov 20, 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
B: Hemagglutinin
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18211
Polymers103,0574
Non-polymers3,1257
Water00
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)318,54733
Polymers309,17212
Non-polymers9,37521
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area56650 Å2
ΔGint-82 kcal/mol
Surface area119670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.842, 130.842, 189.344
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: 35418.867 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: 20153.393 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: 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)

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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.: 3
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.: 3
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 , 1 types, 1 molecules

#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 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: 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: 3.205→45.42 Å / Num. obs: 29818 / % possible obs: 98.8 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.072 / Rrim(I) all: 0.158 / Net I/σ(I): 10.17
Reflection shellResolution: 3.205→3.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2918 / CC1/2: 0.596 / Rpim(I) all: 0.581 / Rrim(I) all: 1.287 / % possible all: 97.6

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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: 3.21→45.42 Å / SU ML: 0.4178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8779
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 2000 6.72 %random
Rwork0.2328 ---
obs0.2362 29771 98.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.21→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 206 0 7165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337319
X-RAY DIFFRACTIONf_angle_d0.67429934
X-RAY DIFFRACTIONf_chiral_restr0.04761141
X-RAY DIFFRACTIONf_plane_restr0.00471269
X-RAY DIFFRACTIONf_dihedral_angle_d10.93991082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.290.40061430.37931928X-RAY DIFFRACTION96.73
3.29-3.370.3051440.28821981X-RAY DIFFRACTION99.86
3.37-3.470.39611400.32821963X-RAY DIFFRACTION97.72
3.47-3.590.37251430.26781985X-RAY DIFFRACTION99.72
3.59-3.710.33161480.27861998X-RAY DIFFRACTION99.08
3.71-3.860.33721380.26431988X-RAY DIFFRACTION99.81
3.86-4.040.35661360.26141934X-RAY DIFFRACTION96.41
4.04-4.250.30711420.22282002X-RAY DIFFRACTION99.77
4.25-4.520.24551450.19721990X-RAY DIFFRACTION99.53
4.52-4.870.22061390.17522002X-RAY DIFFRACTION99.67
4.87-5.350.2271450.18662002X-RAY DIFFRACTION99.63
5.35-6.130.28921410.20312007X-RAY DIFFRACTION99.4
6.13-7.710.29851470.23392012X-RAY DIFFRACTION99.45
7.72-45.420.21361490.22141979X-RAY DIFFRACTION97.26

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