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- PDB-5e34: Crystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D... -

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Basic information

Entry
Database: PDB / ID: 5.0E+34
TitleCrystal structure of H5 hemagglutinin mutant (N224K, Q226L, N158D and L133a deletion) from the influenza virus A/chicken/Vietnam/NCVD-093/2008 (H5N1) with LSTa
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 / 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; 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: 2.7 Å
AuthorsZhu, X. / Wilson, I.A.
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: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_oper_list / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _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 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
Revision 2.2Oct 16, 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)59,5745
Polymers58,4572
Non-polymers1,1173
Water1,62190
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,72215
Polymers175,3716
Non-polymers3,3519
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area33280 Å2
ΔGint-114 kcal/mol
Surface area61420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.824, 130.824, 133.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11B-210-

HOH

21B-211-

HOH

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Components

#1: Protein Hemagglutinin / HEMAGGLUTININ HA1 CHAIN


Mass: 37663.824 Da / Num. of mol.: 1 / Fragment: UNP residues 17-346 / Mutation: N224K, Q226L, N158D and L133a deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/NCVD-093/2008(H5N1))
Strain: A/chicken/Vietnam/NCVD-093/2008(H5N1) / Gene: HA / Plasmid: PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C4P282
#2: Protein Hemagglutinin / HEMAGGLUTININ HA2 CHAIN


Mass: 20793.016 Da / Num. of mol.: 1 / Fragment: UNP residues 347-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/chicken/Vietnam/NCVD-093/2008(H5N1) / Gene: HA / Plasmid: BACULOVIRUS / Details (production host): PFASTBAC-HT / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C4P282
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-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/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+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


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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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

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Sample preparation

CrystalDensity Matthews: 5.7 Å3/Da / Density % sol: 78.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2 M ammonium acetate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34678 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rsym value: 0.16 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.71 / % possible all: 79.4

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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: 5.0E+32 / Resolution: 2.7→46.696 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1722 4.99 %
Rwork0.2137 --
obs0.2155 34531 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 74 90 4137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084147
X-RAY DIFFRACTIONf_angle_d1.1715612
X-RAY DIFFRACTIONf_dihedral_angle_d17.7841537
X-RAY DIFFRACTIONf_chiral_restr0.081609
X-RAY DIFFRACTIONf_plane_restr0.005725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7054-2.78510.40641040.35592247X-RAY DIFFRACTION80
2.7851-2.87490.42141320.34612641X-RAY DIFFRACTION95
2.8749-2.97770.34991480.31952743X-RAY DIFFRACTION99
2.9777-3.09690.35741480.2872782X-RAY DIFFRACTION99
3.0969-3.23780.31131430.26962771X-RAY DIFFRACTION99
3.2378-3.40840.32471600.24212753X-RAY DIFFRACTION99
3.4084-3.62190.27811330.22732805X-RAY DIFFRACTION100
3.6219-3.90140.2481440.19122795X-RAY DIFFRACTION100
3.9014-4.29380.19611640.16742781X-RAY DIFFRACTION100
4.2938-4.91450.18761420.15192822X-RAY DIFFRACTION100
4.9145-6.18950.2191600.19162803X-RAY DIFFRACTION100
6.1895-46.70340.19091440.19512866X-RAY DIFFRACTION100

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