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- PDB-6gol: Three dimensional structure of a novel influenza hemagglutinin tr... -

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Basic information

Entry
Database: PDB / ID: 6gol
TitleThree dimensional structure of a novel influenza hemagglutinin tri-stalk protein
ComponentsHemagglutinin tri-stalk
KeywordsVIRAL PROTEIN / Hemagglutinin stem / Long alpha helix / Influenza / Post-fusion conformation / Tri-stalk protein
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKirsteina, A. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
ERAF 1.1.1.1/16/A/054 Latvia
CitationJournal: PLoS ONE / Year: 2018
Title: Structure and applications of novel influenza HA tri-stalk protein for evaluation of HA stem-specific immunity.
Authors: Lu, I.N. / Kirsteina, A. / Farinelle, S. / Willieme, S. / Tars, K. / Muller, C.P. / Kazaks, A.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

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Assembly

Deposited unit
A: Hemagglutinin tri-stalk


Theoretical massNumber of molelcules
Total (without water)8,5551
Polymers8,5551
Non-polymers00
Water1,02757
1
A: Hemagglutinin tri-stalk

A: Hemagglutinin tri-stalk

A: Hemagglutinin tri-stalk


Theoretical massNumber of molelcules
Total (without water)25,6643
Polymers25,6643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.800, 41.800, 90.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Hemagglutinin tri-stalk


Mass: 8554.573 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/VRDL69/2009(H1N1))
Production host: Escherichia coli (E. coli) / References: UniProt: D3G5J5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0 M ammonium sulfate and 0.1 M Bis-Tris, pH 5.5, protein 10 mg/mL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2015 / Details: RH-COATED TOROIDAL SI MIRROR
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→23.12 Å / Num. obs: 9803 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1439 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HTM

1htm


Resolution: 1.7→23.12 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.352 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21914 473 4.8 %RANDOM
Rwork0.17771 ---
obs0.17959 9323 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.7→23.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms537 0 0 58 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.019545
X-RAY DIFFRACTIONr_bond_other_d0.0030.02504
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.957735
X-RAY DIFFRACTIONr_angle_other_deg1.08431171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.499564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1142630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17815104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.379152
X-RAY DIFFRACTIONr_chiral_restr0.1290.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02104
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_it3.6433.512259
X-RAY DIFFRACTIONr_mcbond_other3.6283.497258
X-RAY DIFFRACTIONr_mcangle_it5.4085.243322
X-RAY DIFFRACTIONr_mcangle_other5.4095.258323
X-RAY DIFFRACTIONr_scbond_it4.5443.897286
X-RAY DIFFRACTIONr_scbond_other4.5363.908287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7745.659413
X-RAY DIFFRACTIONr_long_range_B_refined8.29840.899638
X-RAY DIFFRACTIONr_long_range_B_other8.29840.708633
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 38 -
Rwork0.322 697 -
obs--100 %

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