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- PDB-5xla: The structure of hemagglutinin G228S mutant from an avian-origin ... -

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Basic information

Entry
Database: PDB / ID: 5xla
TitleThe structure of hemagglutinin G228S mutant from an avian-origin H4N6 influenza virus in complex with human receptor analog LSTc
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / H4 hemagglutinin / influenza virus / receptor binding
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 / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSong, H. / Qi, J. / Gao, G.F.
CitationJournal: Cell Rep / Year: 2017
Title: Avian-to-Human Receptor-Binding Adaptation by Influenza A Virus Hemagglutinin H4
Authors: Song, H. / Qi, J. / Xiao, H. / Bi, Y. / Zhang, W. / Xu, Y. / Wang, F. / Shi, Y. / Gao, G.F.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 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 1.5Nov 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 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7036
Polymers112,6422
Non-polymers1,0614
Water9,728540
1
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8513
Polymers56,3211
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-0 kcal/mol
Surface area23800 Å2
MethodPISA
2
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8513
Polymers56,3211
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint1 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.722, 100.722, 686.660
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-888-

HOH

21A-914-

HOH

31B-1001-

HOH

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Components

#1: Protein Hemagglutinin


Mass: 56320.773 Da / Num. of mol.: 2 / Fragment: UNP residues 17-519 / Mutation: G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*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.: 2
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: 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.: 2
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris (pH 6.5) and 20% (w/v) PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 79407 / % possible obs: 100 % / Redundancy: 10.4 % / Net I/σ(I): 20.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.791 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 2.1→43.266 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.24 3987 5.02 %
Rwork0.2103 --
obs0.2118 79407 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7722 0 70 540 8332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077962
X-RAY DIFFRACTIONf_angle_d1.06310788
X-RAY DIFFRACTIONf_dihedral_angle_d14.6522910
X-RAY DIFFRACTIONf_chiral_restr0.0441186
X-RAY DIFFRACTIONf_plane_restr0.0051430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0978-2.12330.31931230.26762532X-RAY DIFFRACTION98
2.1233-2.15020.2651520.25092685X-RAY DIFFRACTION100
2.1502-2.17850.28961480.24992645X-RAY DIFFRACTION100
2.1785-2.20840.25591230.25242671X-RAY DIFFRACTION100
2.2084-2.23990.24851430.24362683X-RAY DIFFRACTION100
2.2399-2.27330.27831420.23842622X-RAY DIFFRACTION100
2.2733-2.30890.27641460.23742676X-RAY DIFFRACTION100
2.3089-2.34670.28921310.23862690X-RAY DIFFRACTION100
2.3467-2.38720.29331510.23442653X-RAY DIFFRACTION100
2.3872-2.43060.26871450.2352653X-RAY DIFFRACTION100
2.4306-2.47730.2441240.2212680X-RAY DIFFRACTION100
2.4773-2.52790.27821580.22692691X-RAY DIFFRACTION100
2.5279-2.58280.26221400.22532680X-RAY DIFFRACTION100
2.5828-2.64290.25121420.22842665X-RAY DIFFRACTION100
2.6429-2.7090.25791430.22632656X-RAY DIFFRACTION100
2.709-2.78220.33371430.22492693X-RAY DIFFRACTION100
2.7822-2.86410.23461530.21832692X-RAY DIFFRACTION100
2.8641-2.95650.26661450.22042707X-RAY DIFFRACTION100
2.9565-3.06210.25911370.2212680X-RAY DIFFRACTION100
3.0621-3.18470.28261410.22372686X-RAY DIFFRACTION100
3.1847-3.32960.24061670.21532695X-RAY DIFFRACTION100
3.3296-3.50510.23031350.20862718X-RAY DIFFRACTION100
3.5051-3.72460.25721330.20342739X-RAY DIFFRACTION100
3.7246-4.0120.2051350.19352720X-RAY DIFFRACTION100
4.012-4.41530.18311350.17372752X-RAY DIFFRACTION100
4.4153-5.05340.17991470.1672755X-RAY DIFFRACTION100
5.0534-6.36350.22091580.19452793X-RAY DIFFRACTION100
6.3635-43.27540.20741470.20352908X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.427 Å / Origin y: 338.7767 Å / Origin z: 748.0833 Å
111213212223313233
T0.1651 Å20.0185 Å2-0.0236 Å2-0.1806 Å20.0079 Å2--0.1997 Å2
L0.231 °2-0.0759 °2-0.1939 °2-0.1364 °20.1216 °2--0.093 °2
S0.0276 Å °0.0895 Å °0.0251 Å °-0.0843 Å °-0.0179 Å °-0.0102 Å °-0.0468 Å °-0.0272 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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