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Basic information

Entry
Database: PDB / ID: 4wss
TitleThe crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998 in complex with LSTa
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / influenza virus / hemagglutinin / H6
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 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
3'-sialyl-N-acetyllactosamine / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_name_com / entity_src_gen / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / 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_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 / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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 2.1Dec 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 / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
E: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,66418
Polymers347,2436
Non-polymers4,42112
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,6059
Polymers173,6213
Non-polymers1,9846
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint-9 kcal/mol
Surface area60220 Å2
MethodPISA
2
E: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,0599
Polymers173,6213
Non-polymers2,4376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-7 kcal/mol
Surface area61730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.967, 134.779, 122.622
Angle α, β, γ (deg.)90.00, 112.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23E
14A
24D
15A
25F
16B
26C
17B
27E
18B
28D
19B
29F
110C
210E
111C
211D
112C
212F
113E
213D
114E
214F
115D
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA1 - 4975 - 501
21ASNASNBB1 - 4975 - 501
12ARGARGAA1 - 4985 - 502
22ARGARGCC1 - 4985 - 502
13ASNASNAA1 - 4975 - 501
23ASNASNED1 - 4975 - 501
14ARGARGAA1 - 4985 - 502
24ARGARGDE1 - 4985 - 502
15ARGARGAA1 - 4985 - 502
25ARGARGFF1 - 4985 - 502
16LEULEUBB1 - 4965 - 500
26LEULEUCC1 - 4965 - 500
17ASNASNBB1 - 4975 - 501
27ASNASNED1 - 4975 - 501
18ASNASNBB1 - 4975 - 501
28ASNASNDE1 - 4975 - 501
19ASNASNBB1 - 4975 - 501
29ASNASNFF1 - 4975 - 501
110ARGARGCC1 - 4985 - 502
210ARGARGED1 - 4985 - 502
111ARGARGCC1 - 4985 - 502
211ARGARGDE1 - 4985 - 502
112ARGARGCC1 - 4985 - 502
212ARGARGFF1 - 4985 - 502
113ARGARGED1 - 4985 - 502
213ARGARGDE1 - 4985 - 502
114ARGARGED1 - 4985 - 502
214ARGARGFF1 - 4985 - 502
115ARGARGDE1 - 4985 - 502
215ARGARGFF1 - 4985 - 502

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Hemagglutinin /


Mass: 57873.789 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/New York/14677-13/1998(H6N2))
Strain: A/chicken/New York/14677-13/1998(H6N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0A3A5
#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.: 2 / Source method: obtained synthetically
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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-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/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M ammonium fluoride and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.2 Å / Num. obs: 92840 / % possible obs: 98.5 % / Redundancy: 3.2 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.8→45.2 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / SU B: 33.852 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25402 4650 5 %RANDOM
Rwork0.21957 ---
obs0.22128 88190 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.42 Å2
2--0.39 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23153 0 289 0 23442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01924020
X-RAY DIFFRACTIONr_bond_other_d0.0080.0222072
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.95332591
X-RAY DIFFRACTIONr_angle_other_deg1.465350795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08952902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5924.6831166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.073154033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.42115131
X-RAY DIFFRACTIONr_chiral_restr0.0910.23519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0227334
X-RAY DIFFRACTIONr_gen_planes_other0.0060.025629
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_it3.6914.80811644
X-RAY DIFFRACTIONr_mcbond_other3.6854.80711643
X-RAY DIFFRACTIONr_mcangle_it5.9227.20614534
X-RAY DIFFRACTIONr_mcangle_other5.9247.20614535
X-RAY DIFFRACTIONr_scbond_it3.8765.1212374
X-RAY DIFFRACTIONr_scbond_other3.8765.1212374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2937.54418056
X-RAY DIFFRACTIONr_long_range_B_refined9.44238.44226365
X-RAY DIFFRACTIONr_long_range_B_other9.44238.44226366
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)
11A279100.09
12B279100.09
21A277320.1
22C277320.1
31A279600.1
32E279600.1
41A278310.1
42D278310.1
51A269340.1
52F269340.1
61B278210.09
62C278210.09
71B273330.1
72E273330.1
81B275000.09
82D275000.09
91B267500.11
92F267500.11
101C278720.09
102E278720.09
111C275420.1
112D275420.1
121C271020.1
122F271020.1
131E274480.11
132D274480.11
141E270420.11
142F270420.11
151D269250.11
152F269250.11
LS refinement shellResolution: 2.802→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 318 -
Rwork0.31 5945 -
obs--90.1 %
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)
10.18960.0622-0.11240.6293-0.09390.0787-0.03220.0558-0.0641-0.0506-0.0255-0.02630.0076-0.00640.05770.0553-0.001-0.07390.2149-0.03420.1689-26.5689-14.07910.4459
20.0725-0.0026-0.06420.46590.18540.1703-0.025-0.03230.01410.0272-0.02910.04720.04780.03190.05410.07110.0024-0.06530.25140.03140.1379-34.351-15.262439.2027
30.0850.0139-0.12610.5823-0.04760.2026-0.01110.0420.0051-0.0657-0.0024-0.01520.021-0.11570.01350.0856-0.0044-0.10780.2383-0.01370.1579-55.6224-13.193418.1442
40.02970.09710.010.93660.13740.02970.01740.0009-0.01680.0331-0.03770.08040.003-0.05010.02030.0334-0.0208-0.07460.23460.0270.198-40.14599.4363-29.4321
50.26670.1784-0.05050.90020.00240.1088-0.0106-0.0604-0.044-0.0672-0.03720.00970.03940.06290.04790.0580.014-0.04340.2130.02290.1154-12.22897.2169-17.8862
60.1525-0.0985-0.17980.56880.02640.2928-0.06520.0915-0.0184-0.0252-0.04320.00150.0757-0.05110.10840.0661-0.032-0.04130.2242-0.02010.1425-16.63059.9101-47.8907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 2001
2X-RAY DIFFRACTION2B1 - 602
3X-RAY DIFFRACTION3C1 - 605
4X-RAY DIFFRACTION4E1 - 605
5X-RAY DIFFRACTION5D1 - 900
6X-RAY DIFFRACTION6F1 - 605

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