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- PDB-2wr2: structure of influenza H2 avian hemagglutinin with avian receptor -

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Basic information

Entry
Database: PDB / ID: 2wr2
Titlestructure of influenza H2 avian hemagglutinin with avian receptor
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / LIPROPROTEIN
Function / homology
Function and homology information


sialate O-acetylesterase activity / sialate O-acetylesterase / 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 / 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
Hemagglutinin-esterase-fusion glycoprotein
Similarity search - Component
Biological speciesUNIDENTIFIED INFLUENZA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.4 Å
AuthorsLiu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
History
DepositionAug 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)174,7948
Polymers172,7813
Non-polymers2,0135
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-27.67 kcal/mol
Surface area59370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.878, 142.723, 199.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEMAGGLUTININ


Mass: 57593.816 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) UNIDENTIFIED INFLUENZA VIRUS / References: UniProt: D0VWP8*PLUS
#2: 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.: 2
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
#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.: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.9 Å3/Da / Density % sol: 57.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 78786 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.4→29.936 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 3956 5 %
Rwork0.2101 --
obs0.212 78786 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.978 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3435 Å20 Å20 Å2
2--2.0543 Å20 Å2
3---0.2891 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11605 0 133 528 12266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612051
X-RAY DIFFRACTIONf_angle_d1.00616307
X-RAY DIFFRACTIONf_dihedral_angle_d17.5644417
X-RAY DIFFRACTIONf_chiral_restr0.0741778
X-RAY DIFFRACTIONf_plane_restr0.0042110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42930.33641350.28942619X-RAY DIFFRACTION99
2.4293-2.460.35791450.28312614X-RAY DIFFRACTION100
2.46-2.49240.36821430.27722662X-RAY DIFFRACTION100
2.4924-2.52650.33911270.28582651X-RAY DIFFRACTION100
2.5265-2.56260.35941480.26542632X-RAY DIFFRACTION100
2.5626-2.60080.35321300.2712650X-RAY DIFFRACTION100
2.6008-2.64140.32441380.25722639X-RAY DIFFRACTION100
2.6414-2.68470.31310.26042671X-RAY DIFFRACTION100
2.6847-2.7310.33021390.25252615X-RAY DIFFRACTION100
2.731-2.78060.29751420.24632663X-RAY DIFFRACTION100
2.7806-2.8340.32721420.24262625X-RAY DIFFRACTION100
2.834-2.89190.2961350.23492671X-RAY DIFFRACTION100
2.8919-2.95470.30991450.24712635X-RAY DIFFRACTION100
2.9547-3.02330.27611310.24312681X-RAY DIFFRACTION100
3.0233-3.09890.26571390.23422648X-RAY DIFFRACTION100
3.0989-3.18260.28841340.22512686X-RAY DIFFRACTION100
3.1826-3.27610.24161440.21482632X-RAY DIFFRACTION100
3.2761-3.38170.2531340.21192700X-RAY DIFFRACTION100
3.3817-3.50240.29991380.21032680X-RAY DIFFRACTION100
3.5024-3.64240.24411180.19992674X-RAY DIFFRACTION100
3.6424-3.80790.23451640.18812658X-RAY DIFFRACTION100
3.8079-4.00820.21021330.18252687X-RAY DIFFRACTION100
4.0082-4.25870.19771610.17462691X-RAY DIFFRACTION100
4.2587-4.58640.18341240.17352703X-RAY DIFFRACTION100
4.5864-5.0460.23141500.16272717X-RAY DIFFRACTION100
5.046-5.77160.19581570.17652719X-RAY DIFFRACTION100
5.7716-7.25450.2221600.19772758X-RAY DIFFRACTION100
7.2545-29.9380.22521690.21042849X-RAY DIFFRACTION99

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