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Entry
Database: PDB / ID: 4wsr
TitleThe crystal structure of hemagglutinin form A/chicken/New York/14677-13/1998
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 / 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 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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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: Non-polymer description / Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / 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_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 / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Dec 27, 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 / 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_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
Revision 2.2Oct 9, 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
C: Hemagglutinin
E: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,92519
Polymers347,2376
Non-polymers3,68813
Water18,4471024
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,99811
Polymers173,6183
Non-polymers2,3798
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-2 kcal/mol
Surface area61730 Å2
MethodPISA
2
E: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,9288
Polymers173,6183
Non-polymers1,3095
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-16 kcal/mol
Surface area61810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.545, 134.822, 123.093
Angle α, β, γ (deg.)90.00, 113.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-884-

HOH

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: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 498 / Label seq-ID: 5 - 502

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23ED
14AA
24DE
15AA
25FF
16BB
26CC
17BB
27ED
18BB
28DE
19BB
29FF
110CC
210ED
111CC
211DE
112CC
212FF
113ED
213DE
114ED
214FF
115DE
215FF

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: 57872.797 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.: 4 / 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: 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.: 9 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M ammonium fluoride, 20% (w/v) PEG 3350

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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: Mar 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48 Å / Num. obs: 129493 / % possible obs: 99 % / Redundancy: 3.8 % / Net I/σ(I): 30.6

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementResolution: 2.5→48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 23.103 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.528 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24617 6504 5 %RANDOM
Rwork0.20997 ---
obs0.21176 122862 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.83 Å2
2--1.76 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23168 0 238 1024 24430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01923984
X-RAY DIFFRACTIONr_bond_other_d0.0080.0222067
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9532539
X-RAY DIFFRACTIONr_angle_other_deg1.499350763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.13852904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06324.6621167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.298154040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2115133
X-RAY DIFFRACTIONr_chiral_restr0.0910.23506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0227355
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025634
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_it3.2884.05711649
X-RAY DIFFRACTIONr_mcbond_other3.2814.05611648
X-RAY DIFFRACTIONr_mcangle_it5.236.0714542
X-RAY DIFFRACTIONr_mcangle_other5.2316.07114543
X-RAY DIFFRACTIONr_scbond_it3.5464.42412333
X-RAY DIFFRACTIONr_scbond_other3.5464.42412333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7466.49917996
X-RAY DIFFRACTIONr_long_range_B_refined9.29832.77527831
X-RAY DIFFRACTIONr_long_range_B_other9.29932.78527790
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)
11A275300.11
12B275300.11
21A273380.11
22C273380.11
31A271500.12
32E271500.12
41A271650.12
42D271650.12
51A266780.12
52F266780.12
61B275300.11
62C275300.11
71B268960.12
72E268960.12
81B271270.12
82D271270.12
91B264820.13
92F264820.13
101C271620.11
102E271620.11
111C271390.12
112D271390.12
121C268610.12
122F268610.12
131E269100.13
132D269100.13
141E266870.13
142F266870.13
151D266930.13
152F266930.13
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 451 -
Rwork0.307 8526 -
obs--93.33 %
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)
10.2056-0.0065-0.09820.6295-0.03160.0533-0.02290.0957-0.0706-0.0292-0.02690.0071-0.0161-0.03480.04980.19690.0034-0.10980.3441-0.03750.2438-26.629854.48429.9749
20.11650.00930.04590.1840.09930.1035-0.00280.02530.04710.0622-0.03060.03160.10920.02110.03350.24920.0016-0.08260.36220.020.1839-34.975452.102238.8756
30.1203-0.0412-0.17810.74090.07840.273-0.05270.0632-0.0128-0.027-0.01250.12050.0441-0.11450.06520.1285-0.0293-0.16490.3562-0.04380.278-56.01553.834217.4235
40.09740.2419-0.07431.9018-0.01950.15170.03490.1765-0.00170.06560.11260.09610.0045-0.2613-0.14740.03610.0342-0.08430.49860.15430.3421-39.131876.3746-29.5878
50.27790.1443-0.21890.40510.00170.24940.08910.0328-0.0180.0441-0.0152-0.0261-0.0047-0.0234-0.07380.20050.0175-0.11050.31660.02270.2356-11.652974.4793-17.8657
60.16660.1214-0.1720.57060.09940.309-0.03760.2384-0.00190.0720.0304-0.08480.0318-0.34490.00720.13060.0078-0.05570.45190.01620.2166-15.789476.6303-48.1622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 927
2X-RAY DIFFRACTION2B1 - 919
3X-RAY DIFFRACTION3C1 - 875
4X-RAY DIFFRACTION4E1 - 785
5X-RAY DIFFRACTION5D1 - 912
6X-RAY DIFFRACTION6F1 - 2206

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