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- PDB-5xld: The structure of hemagglutinin Q226L-G228S mutant from an avian-o... -

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Basic information

Entry
Database: PDB / ID: 5xld
TitleThe structure of hemagglutinin Q226L-G228S mutant from an avian-origin H4N6 influenza virus in complex with human receptor analog LSTc
Components(Hemagglutinin) x 2
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 / 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 / membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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
6'-sialyl-N-acetyllactosamine / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSong, H. / Qi, J. / Gao, F.G.
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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
C: Hemagglutinin
B: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,88210
Polymers112,6484
Non-polymers2,2346
Water6,143341
1
A: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4415
Polymers56,3242
Non-polymers1,1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-24 kcal/mol
Surface area24080 Å2
MethodPISA
2
B: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4415
Polymers56,3242
Non-polymers1,1173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-23 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.413, 100.413, 686.914
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
11D-780-

HOH

21D-781-

HOH

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Components

#1: Protein Hemagglutinin /


Mass: 35981.516 Da / Num. of mol.: 2 / Fragment: UNP residues 17-343 / Mutation: Q226L, G228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS
#2: Protein Hemagglutinin /


Mass: 20342.391 Da / Num. of mol.: 2 / Fragment: UNP residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/Czechoslovakia/1956 H4N6)
Strain: A/Duck/Czechoslovakia/1956 H4N6 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A3KF09, UniProt: P19696*PLUS
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate (pH 6.0) and 14% (w/v) PEG 4,000

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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: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 60153 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 19.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 4 / Rsym value: 0.689 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HA0

1ha0


Resolution: 2.3→42.73 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.52
RfactorNum. reflection% reflection
Rfree0.251 3037 5.05 %
Rwork0.214 --
obs0.216 60153 99.7 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 33.6 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7379 Å20 Å20 Å2
2--7.7379 Å20 Å2
3----15.4758 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7728 0 148 341 8217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068050
X-RAY DIFFRACTIONf_angle_d1.12210908
X-RAY DIFFRACTIONf_dihedral_angle_d16.8782992
X-RAY DIFFRACTIONf_chiral_restr0.0681212
X-RAY DIFFRACTIONf_plane_restr0.0041432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.33620.27421320.24362588X-RAY DIFFRACTION99
2.3362-2.37450.36251160.252542X-RAY DIFFRACTION100
2.3745-2.41540.2991430.26012578X-RAY DIFFRACTION100
2.4154-2.45940.28761340.24542552X-RAY DIFFRACTION100
2.4594-2.50670.30311410.24782563X-RAY DIFFRACTION100
2.5067-2.55780.31211230.23622551X-RAY DIFFRACTION100
2.5578-2.61340.26221290.2412541X-RAY DIFFRACTION100
2.6134-2.67420.25571600.2422571X-RAY DIFFRACTION100
2.6742-2.74110.30571360.23532578X-RAY DIFFRACTION100
2.7411-2.81520.28211250.2342570X-RAY DIFFRACTION100
2.8152-2.8980.27891560.23342572X-RAY DIFFRACTION100
2.898-2.99150.30061490.2342565X-RAY DIFFRACTION100
2.9915-3.09840.28261370.23432573X-RAY DIFFRACTION100
3.0984-3.22240.27561510.23542574X-RAY DIFFRACTION100
3.2224-3.3690.24681380.21462591X-RAY DIFFRACTION100
3.369-3.54660.26051280.21522611X-RAY DIFFRACTION100
3.5466-3.76870.20441470.2012604X-RAY DIFFRACTION100
3.7687-4.05940.2111310.18872618X-RAY DIFFRACTION100
4.0594-4.46750.23331480.17342629X-RAY DIFFRACTION100
4.4675-5.11310.17641320.17182664X-RAY DIFFRACTION100
5.1131-6.43840.25251510.20462676X-RAY DIFFRACTION100
6.4384-42.73990.2421300.22342805X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -72.9665 Å / Origin y: 337.6914 Å / Origin z: 747.6565 Å
111213212223313233
T0.1131 Å20.0151 Å2-0.017 Å2-0.1107 Å20.0096 Å2--0.141 Å2
L0.139 °2-0.0522 °2-0.1308 °2-0.093 °20.1063 °2--0.0848 °2
S0.0024 Å °0.0589 Å °0.0004 Å °-0.0626 Å °-0.0308 Å °0.0025 Å °-0.0416 Å °-0.0302 Å °-0.0027 Å °
Refinement TLS groupSelection details: ALL

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