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- PDB-6pd5: Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 6pd5
TitleCrystal Structure of a H5N1 influenza virus hemagglutinin at pH 6.5
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Influenza / H5
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
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / 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: 2.39 Å
AuthorsAntanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography.
Authors: Antanasijevic, A. / Durst, M.A. / Lavie, A. / Caffrey, M.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,11119
Polymers59,8931
Non-polymers2,21818
Water1,892105
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,33357
Polymers179,6803
Non-polymers6,65354
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area24740 Å2
ΔGint-460 kcal/mol
Surface area62220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.056, 108.056, 419.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1108-

SO4

21A-1109-

SO4

31A-1109-

SO4

41A-1239-

HOH

51A-1305-

HOH

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Components

#1: Protein Hemagglutinin /


Mass: 59893.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/4/2003(H5N1))
Strain: A/chicken/Vietnam/4/2003(H5N1) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q1KHJ8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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.: 4
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
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: 3.94 Å3/Da / Density % sol: 68.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM cacodylate, pH 6.5, 200 mM sodium chloride, 2 M ammonium sulfate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. obs: 37825 / % possible obs: 99.5 % / Redundancy: 9.14 % / CC1/2: 0.997 / Rrim(I) all: 0.163 / Net I/σ(I): 12.29
Reflection shellResolution: 2.39→2.52 Å / Redundancy: 8.65 % / Mean I/σ(I) obs: 2.57 / Num. unique obs: 5929 / CC1/2: 0.857 / Rrim(I) all: 1.764 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FK0

2fk0


Resolution: 2.39→29.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 16.492 / SU ML: 0.301 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.219
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 1828 4.9 %RANDOM
Rwork0.2132 ---
obs0.2156 35486 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 192.98 Å2 / Biso mean: 58.252 Å2 / Biso min: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å2-0 Å2
2--0.07 Å2-0 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 2.39→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 129 105 4166
Biso mean--116.36 49.72 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134160
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173641
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.6615644
X-RAY DIFFRACTIONr_angle_other_deg1.2661.5968511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7135493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11623.877227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72915703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3931519
X-RAY DIFFRACTIONr_chiral_restr0.0670.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024597
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02834
LS refinement shellResolution: 2.39→2.452 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 107 -
Rwork0.387 2585 -
all-2692 -
obs--97.15 %

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