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- PDB-4xqu: Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10... -

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Basic information

Entry
Database: PDB / ID: 4xqu
TitleCrystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza virus in complex with 3'-SLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsTzarum, N. / Zhang, H. / Zhu, X. / Wilson, I.A.
CitationJournal: Cell Host Microbe / Year: 2015
Title: A Human-Infecting H10N8 Influenza Virus Retains a Strong Preference for Avian-type Receptors.
Authors: Zhang, H. / de Vries, R.P. / Tzarum, N. / Zhu, X. / Yu, W. / McBride, R. / Paulson, J.C. / Wilson, I.A.
History
DepositionJan 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / 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_oper_list / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Sep 1, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / 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
Revision 2.2Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,64714
Polymers169,3146
Non-polymers3,3338
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36440 Å2
ΔGint-117 kcal/mol
Surface area58880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.874, 245.853, 70.995
Angle α, β, γ (deg.)90.000, 112.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1


Mass: 35682.258 Da / Num. of mol.: 3 / Fragment: residues 18-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi/IPB13/2013(H10N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A059T4A1
#2: Protein Hemagglutinin HA2


Mass: 20755.818 Da / Num. of mol.: 3 / Fragment: residues 341-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Jiangxi/IPB13/2013(H10N8) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0A059T4A1

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Sugars , 4 types, 8 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-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_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#6: 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.: 3 / Source method: obtained synthetically / 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

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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: 3.09 Å3/Da / Density % sol: 60.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M NaSCN, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0716 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 31215 / % possible obs: 95.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.102 / Rrim(I) all: 0.18 / Χ2: 1.445 / Net I/av σ(I): 8.363 / Net I/σ(I): 5 / Num. measured all: 86794
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.312.10.56914990.650.4480.7270.75891.7
3.31-3.372.20.50515130.7330.3950.6440.72892.3
3.37-3.432.30.50814450.7240.3850.6410.93891.4
3.43-3.52.30.50814940.6980.3890.6440.92890.5
3.5-3.582.60.53915850.7570.3940.6710.94996.8
3.58-3.662.80.42215740.7930.3050.5230.94298.3
3.66-3.752.70.32315770.8360.2290.3981.02697.8
3.75-3.852.90.37615960.8360.2630.4611.05897.7
3.85-3.972.80.30715760.8670.2180.3781.17497.3
3.97-4.0930.25815680.9290.1780.3151.20596.6
4.09-4.242.90.21915850.9360.1520.2681.35697.3
4.24-4.412.90.17715840.9630.1240.2171.5797.1
4.41-4.612.60.14515350.970.1050.181.62594.3
4.61-4.853.10.14815870.9710.0990.1791.74398
4.85-5.163.10.14415860.9730.0950.1731.67298.6
5.16-5.563.10.13616110.9750.090.1641.60998.1
5.56-6.113.10.13415640.9730.0890.1611.47997.3
6.11-72.80.11315590.9790.0790.1391.67793
7-8.813.20.09116000.9890.0610.112.20398.3
8.81-502.90.05615770.9950.0390.0692.98995.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHENIXphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XQ5

4xq5


Resolution: 3.25→48.386 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2612 1572 5.04 %
Rwork0.2171 --
obs0.2193 31164 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.21 Å2 / Biso mean: 86.9092 Å2 / Biso min: 38.19 Å2
Refinement stepCycle: final / Resolution: 3.25→48.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11371 0 222 0 11593
Biso mean--113.88 --
Num. residues----1453
LS refinement shellResolution: 3.2082→3.3118 Å /
RfactorNum. reflection
Rfree0.4368 97
Rwork0.3242 1772

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