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- PDB-7qa4: Crystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglut... -

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Basic information

Entry
Database: PDB / ID: 7qa4
TitleCrystal structure of stabilized H3N2 A/Hong Kong/1/1968 Hemagglutinin at 2.2 Angstrom
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Influenza / Hemagglutinin / Stabilized / Fusion protein / UNKNOWN FUNCTION
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
Similarity search - Domain/homology
NITRATE ION / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsMilder, F.J. / Langedijk, J.P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentHHSO100201700018C United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Universal stabilization of the influenza hemagglutinin by structure-based redesign of the pH switch regions.
Authors: Milder, F.J. / Jongeneelen, M. / Ritschel, T. / Bouchier, P. / Bisschop, I.J.M. / de Man, M. / Veldman, D. / Le, L. / Kaufmann, B. / Bakkers, M.J.G. / Juraszek, J. / Brandenburg, B. / Langedijk, J.P.M.
History
DepositionNov 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7617
Polymers57,1321
Non-polymers2,6296
Water2,414134
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,28321
Polymers171,3953
Non-polymers7,88818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23630 Å2
ΔGint89 kcal/mol
Surface area62470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.094, 154.094, 154.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-602-

NO3

21A-825-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hemagglutinin


Mass: 57131.680 Da / Num. of mol.: 1 / Fragment: Hemagglutinin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q91MA7

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Sugars , 4 types, 5 molecules

#2: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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: obtained synthetically / 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

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Non-polymers , 2 types, 135 molecules

#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7455.1
2
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20.00 %w/v PEG 3350, 0.2 M LiNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999924 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999924 Å / Relative weight: 1
ReflectionResolution: 2.192→108.96 Å / Num. obs: 31315 / % possible obs: 100 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 24.9
Reflection shellResolution: 2.192→108.96 Å / Redundancy: 26.2 % / Rmerge(I) obs: 2.977 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 31315 / Rsym value: 2.977 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: none

Resolution: 2.19→108.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 13.987 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1577 5 %RANDOM
Rwork0.1984 ---
obs0.201 29737 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 158.29 Å2 / Biso mean: 66.571 Å2 / Biso min: 39.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.19→108.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 169 134 4141
Biso mean--100.26 58.9 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134081
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173568
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.7055573
X-RAY DIFFRACTIONr_angle_other_deg1.1721.6268312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10922.991214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09515630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7271524
X-RAY DIFFRACTIONr_chiral_restr0.0560.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024533
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02840
LS refinement shellResolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 127 -
Rwork0.292 2148 -
all-2275 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05951.14821.02641.33161.15151.09880.0484-0.11050.11440.1886-0.07530.05150.04510.02730.02690.2607-0.0228-0.07720.227-0.05380.1958-7.151-17.962.805
23.4531-0.21180.82982.19350.66712.66120.06110.2722-0.2683-0.1274-0.09550.31170.0137-0.24750.03450.0816-0.0516-0.00220.1066-0.03650.1076-47.618-49.812-25.27
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 56
2X-RAY DIFFRACTION1A272 - 502
3X-RAY DIFFRACTION2A57 - 271

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