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- PDB-6tva: Crystal structure of the haemagglutinin from a transmissible H10N... -

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Basic information

Entry
Database: PDB / ID: 6tva
TitleCrystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland in complex with avian receptor analogue, 3'-SLN
Components(Haemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / receptor binding / fusion of virus membrane with host plasma membrane
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / 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 / metal ion binding
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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhang, J. / Xiong, X. / Purkiss, A. / Walker, P. / Gamblin, S. / Skehel, J.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell Host Microbe / Year: 2020
Title: Hemagglutinin Traits Determine Transmission of Avian A/H10N7 Influenza Virus between Mammals.
Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / ...Authors: Herfst, S. / Zhang, J. / Richard, M. / McBride, R. / Lexmond, P. / Bestebroer, T.M. / Spronken, M.I.J. / de Meulder, D. / van den Brand, J.M. / Rosu, M.E. / Martin, S.R. / Gamblin, S.J. / Xiong, X. / Peng, W. / Bodewes, R. / van der Vries, E. / Osterhaus, A.D.M.E. / Paulson, J.C. / Skehel, J.J. / Fouchier, R.A.M.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Haemagglutinin HA1
B: Haemagglutinin HA2
C: Haemagglutinin HA1
D: Haemagglutinin HA2
E: Haemagglutinin HA1
F: Haemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,06315
Polymers164,0236
Non-polymers4,0419
Water21,2941182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37210 Å2
ΔGint-133 kcal/mol
Surface area57540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 214.960, 77.310
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Haemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Haemagglutinin HA1


Mass: 34914.547 Da / Num. of mol.: 3
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: A0A0A7HR51
#2: Protein Haemagglutinin HA2


Mass: 19759.715 Da / Num. of mol.: 3
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: A0A0A7HR51

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Sugars , 3 types, 9 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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-Glycam 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
[]{[(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]{}}}}}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.: 5 / Source method: isolated from a natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 1182 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 26%-31% PEG600,0.1M HEPES pH 7.5 or 0.1 M tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→53.74 Å / Num. obs: 211775 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.117 / Net I/σ(I): 9.6
Reflection shellResolution: 1.74→1.77 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10548 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D00

4d00


Resolution: 1.74→53.74 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 10645 5 %RANDOM
Rwork0.2009 201066 --
obs0.2016 211711 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.64 Å2 / Biso mean: 32.8096 Å2 / Biso min: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.14 Å2
2--0.07 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.74→53.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11383 0 269 1182 12834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911910
X-RAY DIFFRACTIONr_bond_other_d00.0210511
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.95816158
X-RAY DIFFRACTIONr_angle_other_deg3.826324510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3351470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62624.697545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.948151959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.161565
X-RAY DIFFRACTIONr_chiral_restr0.060.21806
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213245
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022340
X-RAY DIFFRACTIONr_mcbond_it1.3743.0075898
X-RAY DIFFRACTIONr_mcbond_other1.3713.0075897
X-RAY DIFFRACTIONr_mcangle_it2.1734.5087362
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 774 -
Rwork0.34 14886 -
all-15660 -
obs--99.94 %

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