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- PDB-6ijt: Crystal structure of H5N2 hemagglutinin G228S Q226L mutant with 6... -

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Basic information

Entry
Database: PDB / ID: 6ijt
TitleCrystal structure of H5N2 hemagglutinin G228S Q226L mutant with 6SLN 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
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLin, T.H. / Lee, M.S. / Liu, J.S.
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
DepositionOct 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: 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_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)66,6552
Polymers66,3461
Non-polymers3091
Water00
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,9656
Polymers199,0373
Non-polymers9283
Water0
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 area14200 Å2
ΔGint-48 kcal/mol
Surface area62690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.306, 110.306, 314.111
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: 66345.648 Da / Num. of mol.: 1 / Mutation: G228S, Q226L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A059VBQ9*PLUS
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KJ720208.1 FOR THIS SEQUENCE.

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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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 0.2M MgCl, 18%PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 21438 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.84 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.061 / Rrim(I) all: 0.132 / Net I/σ(I): 11.7
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 2.3 / Rpim(I) all: 1.278 / % possible all: 98.2

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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: 2.9→28.131 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.266 748 5.14 %
Rwork0.2069 --
obs0.2099 14561 87.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→28.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 21 0 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014068
X-RAY DIFFRACTIONf_angle_d1.2065506
X-RAY DIFFRACTIONf_dihedral_angle_d9.8612421
X-RAY DIFFRACTIONf_chiral_restr0.06588
X-RAY DIFFRACTIONf_plane_restr0.007715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.12380.3542920.24561640X-RAY DIFFRACTION53
3.1238-3.43770.31011490.24722713X-RAY DIFFRACTION87
3.4377-3.9340.29191780.2073003X-RAY DIFFRACTION96
3.934-4.9520.24841590.18473154X-RAY DIFFRACTION99
4.952-28.13180.23351700.20393303X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 119.7149 Å / Origin y: -14.7872 Å / Origin z: 61.1359 Å
111213212223313233
T0.1642 Å20.0401 Å2-0.0474 Å2-0.0594 Å20.03 Å2--0.1228 Å2
L0.267 °2-0.101 °20.0403 °2-0.2528 °2-0.0246 °2--0.048 °2
S-0.0246 Å °-0.032 Å °-0.0265 Å °0.0951 Å °0.1061 Å °-0.1417 Å °0.0975 Å °0.0091 Å °0.0104 Å °
Refinement TLS groupSelection details: all

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