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- PDB-6pd3: Crystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6pd3
TitleCrystal Structure of a H5N1 influenza virus hemagglutinin at pH 5.5
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: 2.3 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)62,15020
Polymers59,8361
Non-polymers2,31419
Water2,198122
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,45060
Polymers179,5093
Non-polymers6,94257
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 area25030 Å2
ΔGint-498 kcal/mol
Surface area63480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.383, 109.383, 421.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1109-

SO4

21A-1110-

SO4

31A-1110-

SO4

41A-1256-

HOH

51A-1322-

HOH

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Components

#1: Protein Hemagglutinin /


Mass: 59836.223 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.: 12 / 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.: 122 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM cacodylate, pH 5.5, 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: 2.3→30 Å / Num. obs: 43303 / % possible obs: 99.1 % / Redundancy: 6.02 % / CC1/2: 0.998 / Rrim(I) all: 0.087 / Net I/σ(I): 11.78
Reflection shellResolution: 2.3→2.43 Å / Redundancy: 5.76 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 6554 / CC1/2: 0.884 / Rrim(I) all: 0.785 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FK0

2fk0


Resolution: 2.3→29.79 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.76 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22887 2121 5 %RANDOM
Rwork0.19858 ---
obs0.20014 40483 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20.98 Å20 Å2
2--1.96 Å20 Å2
3----6.35 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 134 122 4188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134155
X-RAY DIFFRACTIONr_bond_other_d00.0173636
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6615636
X-RAY DIFFRACTIONr_angle_other_deg1.2241.5968498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1725491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17823.894226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3351519
X-RAY DIFFRACTIONr_chiral_restr0.0630.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024584
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02831
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2056.3771964
X-RAY DIFFRACTIONr_mcbond_other5.2056.3751963
X-RAY DIFFRACTIONr_mcangle_it7.6949.5522452
X-RAY DIFFRACTIONr_mcangle_other7.6939.5542453
X-RAY DIFFRACTIONr_scbond_it7.2517.312191
X-RAY DIFFRACTIONr_scbond_other7.2517.3122192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.71510.6643183
X-RAY DIFFRACTIONr_long_range_B_refined13.67172.4114263
X-RAY DIFFRACTIONr_long_range_B_other13.66972.4324264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 140 -
Rwork0.396 2665 -
obs--88.12 %

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