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- PDB-5yt9: Crystal structure of H5 hemagglutinin G228S mutant from A/chicken... -

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Basic information

Entry
Database: PDB / ID: 5yt9
TitleCrystal structure of H5 hemagglutinin G228S mutant from A/chicken/Taiwan/0502/2012
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / H5N2
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion membrane / 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: 2.766 Å
AuthorsLin, T.H. / Lee, M.S. / Wu, W.G. / Liu, J.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Taiwan
CitationJournal: To Be Published
Title: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012
Authors: Lin, T.H. / Lee, M.S. / Wu, W.G. / Liu, J.S.
History
DepositionNov 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 22, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)66,5822
Polymers66,3611
Non-polymers2211
Water36020
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,7456
Polymers199,0823
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area13260 Å2
ΔGint-29 kcal/mol
Surface area63690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.810, 111.810, 313.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin


Mass: 66360.625 Da / Num. of mol.: 1 / Mutation: G228S, R327F, K328T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))
Gene: HA / Cell line (production host): sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A059VBQ9*PLUS
#2: 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.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 0.2M MgCl, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.766→30 Å / Num. obs: 19702 / % possible obs: 99.71 % / Redundancy: 2.6 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.43 / CC1/2: 0.806 / Rpim(I) all: 0.346 / Rrim(I) all: 0.59 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YKC

5ykc


Resolution: 2.766→29.834 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.24
RfactorNum. reflection% reflection
Rfree0.2721 1025 5.21 %
Rwork0.215 --
obs0.2181 19683 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.766→29.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 14 20 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094064
X-RAY DIFFRACTIONf_angle_d1.0775500
X-RAY DIFFRACTIONf_dihedral_angle_d11.0452428
X-RAY DIFFRACTIONf_chiral_restr0.059586
X-RAY DIFFRACTIONf_plane_restr0.008716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7657-2.91140.34641350.27072616X-RAY DIFFRACTION100
2.9114-3.09370.37241430.27772631X-RAY DIFFRACTION100
3.0937-3.33230.33821350.24972657X-RAY DIFFRACTION100
3.3323-3.6670.29911330.21962640X-RAY DIFFRACTION100
3.667-4.19640.25841480.20212656X-RAY DIFFRACTION100
4.1964-5.28230.21441560.18312683X-RAY DIFFRACTION100
5.2823-29.83570.26671750.21112775X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 120.8483 Å / Origin y: -15.0571 Å / Origin z: 61.5686 Å
111213212223313233
T0.4767 Å2-0.0121 Å2-0.0137 Å2-0.3459 Å20.0655 Å2--0.4389 Å2
L0.9215 °2-0.1912 °2-0.016 °2-0.9373 °20.5235 °2--2.6564 °2
S0.0095 Å °-0.2761 Å °-0.0491 Å °0.345 Å °0.1409 Å °-0.09 Å °0.4602 Å °0.0743 Å °-0.1538 Å °
Refinement TLS groupSelection details: all

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