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- PDB-6zrk: Crystal structure of H8 haemagglutinin -

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Basic information

Entry
Database: PDB / ID: 6zrk
TitleCrystal structure of H8 haemagglutinin
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane
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 A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXiong, X. / Walker, P. / Zhang, J. / Gamblin, S. / Skehel, J.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cold Spring Harb Perspect Med / Year: 2021
Title: Hemagglutinin Structure and Activities.
Authors: Gamblin, S.J. / Vachieri, S.G. / Xiong, X. / Zhang, J. / Martin, S.R. / Skehel, J.J.
History
DepositionJul 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 13, 2021Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0157
Polymers55,4642
Non-polymers2,5515
Water4,486249
1
C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,04621
Polymers166,3926
Non-polymers7,65415
Water1086
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 area38030 Å2
ΔGint-42 kcal/mol
Surface area63470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.739, 98.739, 350.383
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules CD

#1: Protein Hemagglutinin /


Mass: 37008.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/blue-winged teal/Guatemala/CIP049-14/2010(H8N4))
Strain: A/blue-winged teal/Guatemala/CIP049-14/2010(H8N4) / Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: G0KTJ4
#2: Protein Hemagglutinin /


Mass: 18455.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Cell line (production host): Sf9 / Production host: unidentified baculovirus / References: UniProt: A0A5C1ZL56, UniProt: G0KTD9*PLUS

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Sugars , 3 types, 5 molecules

#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}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.: 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
#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 / N-Acetylglucosamine


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

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Non-polymers , 1 types, 249 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.0, 20-22% PEG3350, 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→83.07 Å / Num. obs: 44838 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 6458 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.1data extraction
SCALAdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jsd

1jsd


Resolution: 2→83.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 2249 5 %RANDOM
Rwork0.2242 42386 --
obs0.2259 44635 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.79 Å2 / Biso mean: 44.238 Å2 / Biso min: 22.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2→83.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 169 249 4311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194165
X-RAY DIFFRACTIONr_bond_other_d00.023652
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9895665
X-RAY DIFFRACTIONr_angle_other_deg4.07238556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16725204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14215683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5441522
X-RAY DIFFRACTIONr_chiral_restr0.0780.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214550
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02803
X-RAY DIFFRACTIONr_mcbond_it1.254.2291958
X-RAY DIFFRACTIONr_mcbond_other1.254.2281957
X-RAY DIFFRACTIONr_mcangle_it2.0566.3382444
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 167 -
Rwork0.326 3084 -
all-3251 -
obs--99.54 %

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