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- PDB-5e2y: Crystal structure of H5 hemagglutinin Q226L mutant from the influ... -

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Basic information

Entry
Database: PDB / ID: 5e2y
TitleCrystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/duck/Egypt/10185SS/2010 (H5N1)
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / H5N1 influenza virus / hemagglutinin / receptor binding specificity / transmission / glycan complex
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI099275 United States
CitationJournal: Cell Rep / Year: 2015
Title: Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants.
Authors: Zhu, X. / Viswanathan, K. / Raman, R. / Yu, W. / Sasisekharan, R. / Wilson, I.A.
History
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Other
Revision 1.2Jan 13, 2016Group: Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,09212
Polymers175,5716
Non-polymers2,5216
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31280 Å2
ΔGint-105 kcal/mol
Surface area62200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.796, 235.766, 71.524
Angle α, β, γ (deg.)90.00, 114.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin / / HEMAGGLUTININ HA1 CHAIN


Mass: 37701.578 Da / Num. of mol.: 3 / Fragment: UNP residues 17-345 / Mutation: Q226L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/duck/Egypt/10185SS/2010(H5N1))
Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0
#2: Protein Hemagglutinin / / HEMAGGLUTININ HA2 CHAIN


Mass: 20822.039 Da / Num. of mol.: 3 / Fragment: UNP residues 347-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/duck/Egypt/10185SS/2010(H5N1) / Gene: HA / Plasmid: BACULOVIRUS / Details (production host): PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: G8IPF0

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Sugars , 3 types, 6 molecules

#3: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5][a1221m-1a_1-5]/1-2-1-3/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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: 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

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Non-polymers , 1 types, 179 molecules

#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085 M Tris, pH 8.5, 10% (v/v/) glycerol, 0.17% (w/v) sodium acetate, 21% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 57168 / % possible obs: 86.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.09 / Net I/av σ(I): 15.3 / Net I/σ(I): 15.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 67.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBM

3gbm


Resolution: 2.6→50 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2921 5.12 %
Rwork0.1958 --
obs0.1978 57100 86.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 166 179 12273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112374
X-RAY DIFFRACTIONf_angle_d1.29316748
X-RAY DIFFRACTIONf_dihedral_angle_d16.8774599
X-RAY DIFFRACTIONf_chiral_restr0.0561814
X-RAY DIFFRACTIONf_plane_restr0.0072181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.595-2.63750.34091070.27152058X-RAY DIFFRACTION70
2.6375-2.6830.30461180.25872257X-RAY DIFFRACTION77
2.683-2.73170.28651380.25042382X-RAY DIFFRACTION79
2.7317-2.78430.2921330.24652322X-RAY DIFFRACTION79
2.7843-2.84110.30151310.2572316X-RAY DIFFRACTION77
2.8411-2.90290.33591330.26322171X-RAY DIFFRACTION75
2.9029-2.97040.31121250.2552547X-RAY DIFFRACTION85
2.9704-3.04460.29311060.24982515X-RAY DIFFRACTION85
3.0446-3.12690.28381310.23952613X-RAY DIFFRACTION88
3.1269-3.21890.2711500.22952716X-RAY DIFFRACTION91
3.2189-3.32280.25661480.22492753X-RAY DIFFRACTION93
3.3228-3.44150.28781360.22172799X-RAY DIFFRACTION94
3.4415-3.57920.27241510.2122605X-RAY DIFFRACTION88
3.5792-3.7420.22351470.18652858X-RAY DIFFRACTION96
3.742-3.93910.23591540.18252822X-RAY DIFFRACTION95
3.9391-4.18570.21241440.1772823X-RAY DIFFRACTION95
4.1857-4.50860.18151550.15812777X-RAY DIFFRACTION94
4.5086-4.96160.20741700.15252644X-RAY DIFFRACTION91
4.9616-5.67810.20071450.17152857X-RAY DIFFRACTION96
5.6781-7.1480.21251510.18982689X-RAY DIFFRACTION90
7.148-41.98440.20771480.17382655X-RAY DIFFRACTION88

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