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

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Basic information

Entry
Database: PDB / ID: 6aoq
TitleCrystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin apo form
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 / 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
Hemagglutinin / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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_struct_assembly_gen.asym_id_list / _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 2.1Oct 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

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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)58,90310
Polymers55,8762
Non-polymers3,0288
Water2,288127
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)176,71030
Polymers167,6276
Non-polymers9,08324
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 area43430 Å2
ΔGint9 kcal/mol
Surface area61060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.614, 100.614, 382.620
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 , 4 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: 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.: 5
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, 127 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 3.34 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: 0.1 M CAPS pH 10.5 and 29% PEG 400

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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: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 31953 / % possible obs: 99.9 % / Redundancy: 15.5 % / Biso Wilson estimate: 43 Å2 / CC1/2: 1 / Rpim(I) all: 0.03 / Rsym value: 0.11 / Net I/σ(I): 34.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3148 / CC1/2: 0.93 / Rpim(I) all: 0.22 / Rsym value: 0.84 / % possible all: 100

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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: 2.35→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.878 / SU B: 18.637 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.233 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26157 1626 5.1 %RANDOM
Rwork0.2155 ---
obs0.21791 30220 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.439 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----3.83 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 198 127 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194194
X-RAY DIFFRACTIONr_bond_other_d0.0010.023726
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9965715
X-RAY DIFFRACTIONr_angle_other_deg0.93338722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85524.772197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76915684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2541524
X-RAY DIFFRACTIONr_chiral_restr0.080.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
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_it1.1213.4771968
X-RAY DIFFRACTIONr_mcbond_other1.1213.4781967
X-RAY DIFFRACTIONr_mcangle_it1.8925.2142459
X-RAY DIFFRACTIONr_mcangle_other1.8915.2132460
X-RAY DIFFRACTIONr_scbond_it1.9434.1852226
X-RAY DIFFRACTIONr_scbond_other1.9434.1862227
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4156.243252
X-RAY DIFFRACTIONr_long_range_B_refined7.25270.22216211
X-RAY DIFFRACTIONr_long_range_B_other7.10870.12616154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.342→2.403 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 89 -
Rwork0.287 2232 -
obs--99.7 %
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)
10.5668-0.07650.18610.79990.12762.8570.1265-0.2488-0.25110.34790.1573-0.07270.5470.1753-0.28390.27070.0393-0.11750.14890.08470.209-45.35687.863162.6328
22.50290.58660.12772.6452-0.19393.17070.0198-0.9168-0.07110.71640.2231-0.12070.28590.2683-0.2430.77070.1006-0.20910.59390.05440.0946-39.761314.576992.6172
30.7007-0.280.26490.8018-1.13634.07190.0547-0.1463-0.21990.12770.0931-0.04790.33780.1521-0.14790.2030.0184-0.08530.09770.02510.2147-48.51619.926849.7583
40.90220.181-0.77031.84131.64215.68390.090.1606-0.0884-0.0982-0.05450.00370.536-0.1823-0.03550.2362-0.0058-0.06280.0795-0.05250.2666-52.435910.46599.5658
54.76930.06940.73715.49954.091721.62940.0225-0.03590.0173-0.02090.0447-0.11260.2510.6239-0.06730.1520.0017-0.01750.13980.00570.2758-42.079214.607425.7262
65.0744-0.8414-4.11883.79612.56668.30230.05560.0514-0.4647-0.0816-0.0185-0.04150.08550.0347-0.0370.24560.0529-0.12230.14570.02810.1988-45.684815.963657.5376
70.7475-0.2803-1.61870.60941.59712.2388-0.0096-0.106-0.07090.06560.00650.06420.1848-0.06430.00310.1415-0.0124-0.01050.10510.00620.2325-52.760522.564339.7442
82.1765-1.0179-0.32574.1988-0.51183.3212-0.02550.4118-0.152-0.34610.0091-0.21790.15030.09470.01640.18610.00430.00540.1327-0.09140.2002-45.670616.4567-4.8746
924.8061-18.1971.407914.378-2.53022.26550.89512.0808-0.8903-0.6854-0.87910.6150.0407-0.8457-0.0161.0281-0.007-0.33980.73390.09070.5478-53.793522.1534-15.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 139
2X-RAY DIFFRACTION2A140 - 259
3X-RAY DIFFRACTION3A260 - 325
4X-RAY DIFFRACTION4B1 - 37
5X-RAY DIFFRACTION5B38 - 55
6X-RAY DIFFRACTION6B56 - 71
7X-RAY DIFFRACTION7B72 - 123
8X-RAY DIFFRACTION8B124 - 168
9X-RAY DIFFRACTION9B169 - 173

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