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- PDB-4w8n: The crystal structure of hemagglutinin from a swine influenza vir... -

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Basic information

Entry
Database: PDB / ID: 4w8n
TitleThe crystal structure of hemagglutinin from a swine influenza virus (A/swine/Missouri/2124514/2006)
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Hemagglutinin / Influenza Virus
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / Resolution: 2.9 Å
AuthorsYang, H. / Carney, P.J. / Tumpey, T.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets.
Authors: Pappas, C. / Yang, H. / Carney, P.J. / Pearce, M.B. / Katz, J.M. / Stevens, J. / Tumpey, T.M.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_PDB_model_num / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.dist / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_asym.entity_id / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: 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_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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,04317
Polymers172,6106
Non-polymers2,43311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31640 Å2
ΔGint-109 kcal/mol
Surface area60710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.291, 160.028, 170.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 334
2010C15 - 334
1020A17 - 334
2020E17 - 334
1030B4 - 171
2030D4 - 171
1040B9 - 171
2040F9 - 171
1050C17 - 334
2050E17 - 334
1060D9 - 171
2060F9 - 171

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Hemagglutinin


Mass: 36862.758 Da / Num. of mol.: 3 / Fragment: unp residues 16-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/swine/Missouri/2124514/2006(H2N3) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A9YN66
#2: Protein Hemagglutinin


Mass: 20673.893 Da / Num. of mol.: 3 / Fragment: unp residues 341-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/swine/Missouri/2124514/2006(H2N3) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A9YN66
#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.: 11 / 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

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3000, 0.1M Tris-HCl pH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 41095 / % possible obs: 99.8 % / Redundancy: 7.2 % / Net I/σ(I): 20.4

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.921 / SU B: 49.328 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26224 2170 5 %RANDOM
Rwork0.2326 ---
obs0.23413 41095 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.224 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---4.27 Å20 Å2
3---2.34 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11675 0 154 0 11829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912102
X-RAY DIFFRACTIONr_bond_other_d0.0040.0211233
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.95816397
X-RAY DIFFRACTIONr_angle_other_deg0.874325848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12951465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34624.872585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.577152082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5491564
X-RAY DIFFRACTIONr_chiral_restr0.0770.21787
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213744
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1035.7455878
X-RAY DIFFRACTIONr_mcbond_other4.1035.7445877
X-RAY DIFFRACTIONr_mcangle_it6.5538.6177337
X-RAY DIFFRACTIONr_mcangle_other6.5528.6187338
X-RAY DIFFRACTIONr_scbond_it5.0616.3386224
X-RAY DIFFRACTIONr_scbond_other5.0616.3386224
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1059.2989061
X-RAY DIFFRACTIONr_long_range_B_refined11.2946.48213505
X-RAY DIFFRACTIONr_long_range_B_other11.28946.48913506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A199050.01
12C199050.01
21A198300.02
22E198300.02
31B89940.01
32D89940.01
41B87520.01
42F87520.01
51C198140.02
52E198140.02
61D87550.01
62F87550.01
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 144 -
Rwork0.339 2985 -
obs--99.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1126-0.33460.22044.573-2.38251.5139-0.1153-0.0933-0.0620.07190.2383-0.01040.0844-0.4029-0.1230.3382-0.13050.12970.51450.01610.2214-25.7597.974-0.946
20.37031.1628-0.99215.3076-4.77415.41660.0744-0.01770.00620.1073-0.1206-0.29890.24580.01840.04620.5498-0.21660.02650.4944-0.05230.1383-19.798-32.30631.821
30.61840.1139-0.34182.5182-1.16591.9808-0.21120.00660.1484-0.34490.0809-1.37990.04910.10510.13030.1966-0.14240.25380.4218-0.21561.01537.47611.1755.245
40.353-0.3080.33882.8333-3.38184.3276-0.0215-0.02580.0521-0.8267-0.1418-0.35390.99310.38050.16330.44050.17950.11310.4243-0.11720.32811.225-30.27435.222
50.722-0.93640.23232.7118-1.29952.87550.13030.11730.1178-1.3064-0.0721-0.550.71990.273-0.05821.1354-0.21970.5810.4385-0.17210.4317-3.496-9.25-20.412
60.55590.9919-0.66537.0056-4.31343.5389-0.05990.0469-0.1632-0.16610.0011-0.2040.74930.08540.05870.87260.01410.24620.3192-0.09540.4136-6.536-43.01719.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 320
2X-RAY DIFFRACTION2B4 - 172
3X-RAY DIFFRACTION3C15 - 325
4X-RAY DIFFRACTION4D1 - 172
5X-RAY DIFFRACTION5E17 - 320
6X-RAY DIFFRACTION6F9 - 172

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