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

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Basic information

Entry
Database: PDB / ID: 6tvc
TitleCrystal structure of the haemagglutinin from a transmissible H10N7 seal influenza virus isolated in Netherland
Components
  • Haemagglutinin HA1
  • Haemagglutinin HA2
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 / 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 / membrane
Similarity search - Function
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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
Revision 1.2Nov 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

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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)164,3419
Polymers163,6786
Non-polymers6643
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32150 Å2
ΔGint-177 kcal/mol
Surface area56510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.380, 214.950, 74.670
Angle α, β, γ (deg.)90.000, 97.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haemagglutinin HA1


Mass: 34799.457 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
#3: 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.: 3
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / Source method: isolated from a natural source / Formula: H2O
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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 26%-31% PEG600, 0.1M HEPES pH7.5 or 0.1M tris pH8.0

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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 PILATUS3 6M / 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: 1.84→51.48 Å / Num. obs: 171611 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 1 / Net I/σ(I): 10.8
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 3.4 % / Num. unique obs: 8592 / CC1/2: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d00

4d00


Resolution: 1.84→51.48 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 8385 4.9 %RANDOM
Rwork0.232 163167 --
obs0.233 171552 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 529.52 Å2 / Biso mean: 49.2398 Å2 / Biso min: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-1.08 Å2
2---0.25 Å2-0 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11343 0 42 735 12120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911627
X-RAY DIFFRACTIONr_bond_other_d00.0210335
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.93615750
X-RAY DIFFRACTIONr_angle_other_deg3.86324050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43451467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39624.758538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.453151953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9571563
X-RAY DIFFRACTIONr_chiral_restr0.0610.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213108
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022316
X-RAY DIFFRACTIONr_mcbond_it2.714.6885886
X-RAY DIFFRACTIONr_mcbond_other2.714.6885885
X-RAY DIFFRACTIONr_mcangle_it3.8897.0267347
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 607 -
Rwork0.473 12087 -
all-12694 -
obs--99.89 %

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