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- PDB-5ykc: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 -

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Basic information

Entry
Database: PDB / ID: 5ykc
Titlecrystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / H5N2
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.823 Å
AuthorsLin, T.H. / Lee, M.S. / Wu, W.G.
CitationJournal: To Be Published
Title: crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012
Authors: Lin, T.H. / Lee, M.S. / Wu, W.G.
History
DepositionOct 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _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.ptnr1_label_seq_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 2.1Nov 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,07116
Polymers198,9923
Non-polymers3,07913
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-5 kcal/mol
Surface area65760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.424, 220.103, 186.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemagglutinin


Mass: 66330.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Taiwan/0502/2012(H5N2))
Strain: A/chicken/Taiwan/0502/2012(H5N2) / Production host: unidentified baculovirus / References: UniProt: A0A059VBQ9*PLUS
#2: 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.: 1
Source method: isolated from a genetically manipulated source
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
#3: 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.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KJ720208.1 FOR THIS SEQUENCE.

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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: 2.85 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris, 0.2M MgCl, 14% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.823→29.04 Å / Num. obs: 46855 / % possible obs: 85.41 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.14
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.685 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e2y

5e2y


Resolution: 2.823→29.036 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.94
RfactorNum. reflection% reflection
Rfree0.2725 2431 5.19 %
Rwork0.1973 --
obs0.2011 46839 85.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.823→29.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11892 0 196 4 12092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312380
X-RAY DIFFRACTIONf_angle_d1.26616774
X-RAY DIFFRACTIONf_dihedral_angle_d11.4447370
X-RAY DIFFRACTIONf_chiral_restr0.081814
X-RAY DIFFRACTIONf_plane_restr0.0132178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8234-2.8810.3358790.21631240X-RAY DIFFRACTION41
2.881-2.94360.3478780.25331459X-RAY DIFFRACTION48
2.9436-3.0120.4085810.27841785X-RAY DIFFRACTION58
3.012-3.08720.34171010.25292122X-RAY DIFFRACTION70
3.0872-3.17060.38081300.25922248X-RAY DIFFRACTION75
3.1706-3.26380.36741370.23532402X-RAY DIFFRACTION80
3.2638-3.3690.29211360.22522657X-RAY DIFFRACTION87
3.369-3.48920.31031440.23332923X-RAY DIFFRACTION95
3.4892-3.62860.28071730.20972989X-RAY DIFFRACTION99
3.6286-3.79340.2741780.20483009X-RAY DIFFRACTION99
3.7934-3.9930.28661670.18593036X-RAY DIFFRACTION100
3.993-4.24240.23371650.17623056X-RAY DIFFRACTION100
4.2424-4.56880.21221640.163051X-RAY DIFFRACTION100
4.5688-5.02650.2371760.16683040X-RAY DIFFRACTION100
5.0265-5.74890.26371630.1823080X-RAY DIFFRACTION100
5.7489-7.22450.27321720.20453135X-RAY DIFFRACTION100
7.2245-29.03720.2481870.18233176X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -30.6151 Å / Origin y: -51.1159 Å / Origin z: 17.8827 Å
111213212223313233
T0.218 Å2-0.0075 Å2-0.0658 Å2-0.2802 Å2-0.0605 Å2--0.378 Å2
L0.3843 °2-0.1228 °2-0.1519 °2-1.4892 °20.3986 °2--0.7411 °2
S-0.0133 Å °-0.0942 Å °0.1354 Å °0.1289 Å °0.0658 Å °-0.2276 Å °-0.1396 Å °0.058 Å °-0.0293 Å °
Refinement TLS groupSelection details: all

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