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- PDB-6aov: Crystal structure of the A/Brisbane/10/2007 (H3N2) influenza viru... -

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Basic information

Entry
Database: PDB / ID: 6aov
TitleCrystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin in complex with 6'-SLNLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza A virus / hemagglutinin / mutant / receptor binding / antigenicity
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
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI114730 United States
CitationJournal: PLoS Pathog. / Year: 2017
Title: A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine.
Authors: Wu, N.C. / Zost, S.J. / Thompson, A.J. / Oyen, D. / Nycholat, C.M. / McBride, R. / Paulson, J.C. / Hensley, S.E. / Wilson, I.A.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_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 2.1Oct 4, 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 / pdbx_initial_refinement_model / struct_conn
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
Revision 2.2Nov 13, 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 HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,72210
Polymers55,8762
Non-polymers3,8478
Water8,323462
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules

A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,16730
Polymers167,6276
Non-polymers11,54024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area48160 Å2
ΔGint38 kcal/mol
Surface area60250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.720, 100.720, 385.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35922.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Brisbane/10/2007(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8W891, UniProt: B2VNK2*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 19953.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brisbane/10/2007(H3N2))
Strain: A/Brisbane/10/2007(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8W891, UniProt: C3PR70*PLUS

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Sugars , 5 types, 8 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1039.937 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-2-3/a4-b1_b3-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#7: 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.: 4
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

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Non-polymers , 1 types, 462 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine pH 9 and 41% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 75889 / % possible obs: 99.8 % / Redundancy: 18.5 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 55.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 16 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7485 / CC1/2: 0.94 / Rpim(I) all: 0.23 / Rsym value: 0.92 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000712data processing
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5N

4o5n


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.667 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19563 3862 5.1 %RANDOM
Rwork0.17372 ---
obs0.17481 72000 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.439 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----2.56 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 255 462 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194277
X-RAY DIFFRACTIONr_bond_other_d0.0020.023781
X-RAY DIFFRACTIONr_angle_refined_deg1.5572.0095838
X-RAY DIFFRACTIONr_angle_other_deg0.94738868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8395506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67424.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8341525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
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_it0.9141.831976
X-RAY DIFFRACTIONr_mcbond_other0.9151.831975
X-RAY DIFFRACTIONr_mcangle_it1.4682.742471
X-RAY DIFFRACTIONr_mcangle_other1.4682.742472
X-RAY DIFFRACTIONr_scbond_it1.7922.5432301
X-RAY DIFFRACTIONr_scbond_other1.7922.5432301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0283.7553359
X-RAY DIFFRACTIONr_long_range_B_refined6.84940.94417484
X-RAY DIFFRACTIONr_long_range_B_other6.37939.72117017
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 263 -
Rwork0.24 4987 -
obs--93.48 %
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)
10.3437-0.01440.13360.3557-0.0721.80050.0729-0.1455-0.14140.12180.0686-0.06890.28550.0642-0.14150.13730.0145-0.07850.08310.04370.1492-45.44038.316761.0482
22.17170.16550.04361.22320.02041.44820.0212-0.6648-0.18310.48940.1486-0.31390.33530.1567-0.16990.4690.0595-0.17820.46040.07540.1452-38.483610.652494.3578
30.3706-0.183-1.53682.3374-1.871810.0227-0.0088-0.27890.07280.94010.74850.691-0.96920.0983-0.73970.7280.00130.11730.72520.04690.7126-44.688816.9236103.4059
42.0358-0.18040.03541.5010.10241.13970.0969-0.52430.0230.47780.0899-0.08940.08990.1103-0.18680.34590.0186-0.10350.33840.02390.0787-41.15117.986690.2299
50.3420.01120.1730.2867-0.40811.94610.0749-0.0505-0.12390.01170.0494-0.06530.26150.0562-0.12430.1160.0112-0.0640.05570.01520.1513-48.127810.065750.4497
60.9105-0.3226-0.66091.57331.16333.19320.0320.0428-0.0519-0.08920.0246-0.01770.2518-0.1075-0.05660.1304-0.0134-0.02720.0195-0.03740.1282-52.263410.37759.5246
71.9507-0.00460.97361.57370.846316.43720.0068-0.17930.02340.11820.0694-0.14250.04640.5655-0.07620.09650.0033-0.02570.1142-0.01950.1914-41.561714.573728.4689
88.4471-0.1937-4.18953.03790.28515.3382-0.0691-0.0081-0.21790.08050.0982-0.05150.30970.0659-0.02910.13820.0037-0.05220.07820.01810.1314-47.369516.47662.5498
90.4784-0.1625-1.16730.37891.18958.59190.0311-0.0423-0.04210.0090.03840.00780.01-0.0318-0.06950.0941-0.0049-0.00730.06210.00730.1418-52.646522.526239.7937
101.98410.0173-0.24082.5218-0.90432.4110.01790.1727-0.0622-0.1656-0.0188-0.14550.05860.04550.00090.11070.00540.0090.0466-0.04690.1132-45.214216.5348-4.8158
1118.7751-17.9925-1.162817.4201-0.0268.44031.72751.5355-0.1266-1.5772-1.2570.1993-0.022-1.5549-0.47050.85310.0867-0.41090.51940.11410.7103-53.526822.3086-14.9884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 131
2X-RAY DIFFRACTION2A132 - 192
3X-RAY DIFFRACTION3A193 - 202
4X-RAY DIFFRACTION4A203 - 258
5X-RAY DIFFRACTION5A259 - 325
6X-RAY DIFFRACTION6B1 - 36
7X-RAY DIFFRACTION7B37 - 60
8X-RAY DIFFRACTION8B61 - 71
9X-RAY DIFFRACTION9B72 - 123
10X-RAY DIFFRACTION10B124 - 168
11X-RAY DIFFRACTION11B169 - 173

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