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- PDB-6tjy: Crystal structure of haemagglutinin from (A/seal/Germany/1/2014) ... -

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Basic information

Entry
Database: PDB / ID: 6tjy
TitleCrystal structure of haemagglutinin from (A/seal/Germany/1/2014) seal H10N7 influenza virus
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Host Cell Surface Receptor Binding / Fusion of Virus Membrane with Host Plasma Membrane / Viral Envelope
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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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
DepositionNov 27, 2019Deposition 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 1.2Oct 16, 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 HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,96124
Polymers334,87512
Non-polymers3,08612
Water8,881493
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: Hemagglutinin HA1
J: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,78712
Polymers167,4376
Non-polymers1,3496
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33570 Å2
ΔGint-161 kcal/mol
Surface area57390 Å2
MethodPISA
2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
K: Hemagglutinin HA1
L: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,17412
Polymers167,4376
Non-polymers1,7376
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34740 Å2
ΔGint-164 kcal/mol
Surface area56620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.421, 212.932, 156.901
Angle α, β, γ (deg.)90.000, 101.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin HA1


Mass: 35499.078 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))
Gene: HA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0A7HR51
#2: Protein
Hemagglutinin HA2


Mass: 20313.389 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/harbour seal/Germany/1/2014(H10N7))
Gene: HA / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0A7HNL0, UniProt: A0A0A7HR51*PLUS

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Sugars , 3 types, 9 molecules

#3: 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 natural 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-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.: 3 / Source method: isolated from a natural 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
#6: 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
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, 496 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 2%-4% PEG6000, 0.1M HEPES pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→35.04 Å / Num. obs: 105212 / % possible obs: 98.2 % / Redundancy: 2.8 % / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 2.82→2.87 Å / Num. unique obs: 5226 / CC1/2: 0.96

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Processing

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

4d00


Resolution: 2.82→35.04 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.214 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 5254 5 %RANDOM
Rwork0.2161 99915 --
obs0.2181 105169 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.97 Å2 / Biso mean: 67.7279 Å2 / Biso min: 21.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.82→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22723 0 196 493 23412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01923437
X-RAY DIFFRACTIONr_bond_other_d00.0220590
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.94131768
X-RAY DIFFRACTIONr_angle_other_deg3.878347982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.41752944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88924.8691111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.312153891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.93315127
X-RAY DIFFRACTIONr_chiral_restr0.060.23477
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0226458
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024645
X-RAY DIFFRACTIONr_mcbond_it2.0026.78611791
X-RAY DIFFRACTIONr_mcbond_other2.0026.78611790
X-RAY DIFFRACTIONr_mcangle_it3.42110.17814718
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 354 -
Rwork0.323 7442 -
all-7796 -
obs--98.47 %

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