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- PDB-5yt8: Crystal structure of H5 hemagglutinin with G228S Q226L mutants fr... -

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Basic information

Entry
Database: PDB / ID: 5yt8
TitleCrystal structure of H5 hemagglutinin with G228S Q226L mutants 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 / 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
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: 2.765 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

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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)66,5672
Polymers66,3461
Non-polymers2211
Water1,02757
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,7016
Polymers199,0373
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 area13150 Å2
ΔGint-34 kcal/mol
Surface area63250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.170, 111.170, 313.782
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-701-

HOH

21A-704-

HOH

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Components

#1: Protein Hemagglutinin /


Mass: 66345.648 Da / Num. of mol.: 1 / Mutation: Q226L, Q228S, 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-Acetylglucosamine


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 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris, 0.2M MgCl, 14% 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: 2.765→30 Å / Num. obs: 19535 / % possible obs: 99.8 % / Redundancy: 4.8 % / Net I/σ(I): 20.4
Reflection shellResolution: 2.765→2.87 Å / Redundancy: 4.8 % / Num. unique obs: 1927 / CC1/2: 0.867 / % possible all: 100

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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 / Resolution: 2.765→26.676 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.79
RfactorNum. reflection% reflection
Rfree0.2539 950 5.22 %
Rwork0.1993 --
obs0.2022 18199 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.765→26.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 14 57 4026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094062
X-RAY DIFFRACTIONf_angle_d1.0955497
X-RAY DIFFRACTIONf_dihedral_angle_d9.8472427
X-RAY DIFFRACTIONf_chiral_restr0.059587
X-RAY DIFFRACTIONf_plane_restr0.006715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.765-2.91060.3458810.26281505X-RAY DIFFRACTION58
2.9106-3.09270.33781320.26382479X-RAY DIFFRACTION95
3.0927-3.33110.2891280.23122617X-RAY DIFFRACTION100
3.3311-3.66550.26241350.19962623X-RAY DIFFRACTION100
3.6655-4.19420.24781480.18032627X-RAY DIFFRACTION100
4.1942-5.27750.1991530.16152664X-RAY DIFFRACTION100
5.2775-26.67770.25031730.20222734X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 120.488 Å / Origin y: -14.9728 Å / Origin z: 61.2045 Å
111213212223313233
T0.2612 Å20.0257 Å2-0.0111 Å2-0.1431 Å20.0588 Å2--0.2248 Å2
L0.8228 °2-0.1789 °2-0.0193 °2-0.8046 °20.2943 °2--1.0598 °2
S-0.0373 Å °-0.204 Å °-0.0352 Å °0.2884 Å °0.1418 Å °-0.1214 Å °0.3427 Å °0.0565 Å °-0.0552 Å °
Refinement TLS groupSelection details: all

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