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- PDB-6bkt: Crystal structure of the A/Michigan/15/2014 (H3N2) influenza viru... -

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Basic information

Entry
Database: PDB / ID: 6bkt
TitleCrystal structure of the A/Michigan/15/2014 (H3N2) influenza virus hemagglutinin in complex with 6'-SLN
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / Influenza / Hemagglutinin / Receptor
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
6'-sialyl-N-acetyllactosamine / DI(HYDROXYETHYL)ETHER / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Nat Commun / Year: 2018
Title: A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site.
Authors: Wu, N.C. / Thompson, A.J. / Xie, J. / Lin, C.W. / Nycholat, C.M. / Zhu, X. / Lerner, R.A. / Paulson, J.C. / Wilson, I.A.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / entity_name_com / 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_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 / _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_unobs_or_zero_occ_atoms.label_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,92317
Polymers55,9202
Non-polymers4,00315
Water8,539474
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,10933
Polymers107,7713
Non-polymers9,33930
Water543
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
2
B: Hemagglutinin
hetero molecules

B: Hemagglutinin
hetero molecules

B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,65818
Polymers59,9893
Non-polymers2,67015
Water543
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
3
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,76851
Polymers167,7596
Non-polymers12,00845
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 area50700 Å2
ΔGint-170 kcal/mol
Surface area57450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.354, 100.353, 394.281
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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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 35923.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3
#2: Protein Hemagglutinin /


Mass: 19996.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0Y0S9M3, UniProt: A0A0N9RDU4*PLUS

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Sugars , 3 types, 8 molecules

#3: 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: 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
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-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_b6-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: 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.: 3
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 , 4 types, 481 molecules

#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, and 40% PEG 300

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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: 1.8→50 Å / Num. obs: 71063 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 30 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.06 / Net I/σ(I): 33
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7073 / CC1/2: 0.87 / Rpim(I) all: 0.36 / Rsym value: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000712data processing
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O5N

4o5n


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.827 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19992 3474 4.9 %RANDOM
Rwork0.17377 ---
obs0.17508 67318 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å20 Å2
3----3.54 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 250 474 4594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194298
X-RAY DIFFRACTIONr_bond_other_d0.0020.023967
X-RAY DIFFRACTIONr_angle_refined_deg1.5252.0035844
X-RAY DIFFRACTIONr_angle_other_deg0.94539182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72224.6200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97715700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.721526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
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_it1.0442.2971993
X-RAY DIFFRACTIONr_mcbond_other1.0442.2961992
X-RAY DIFFRACTIONr_mcangle_it1.6283.4362498
X-RAY DIFFRACTIONr_mcangle_other1.6273.4382499
X-RAY DIFFRACTIONr_scbond_it2.0262.9552305
X-RAY DIFFRACTIONr_scbond_other1.9742.932289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1634.2893313
X-RAY DIFFRACTIONr_long_range_B_refined6.80324.49317912
X-RAY DIFFRACTIONr_long_range_B_other6.80324.49217912
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 247 -
Rwork0.258 4949 -
obs--99.98 %
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)
10.2878-0.08590.15270.4179-0.32071.45440.0338-0.1247-0.13520.09070.071-0.01270.22990.0234-0.10490.10230.0199-0.06140.06830.05420.1756-46.57487.706461.5124
21.57520.37910.04441.2647-0.39751.8113-0.0173-0.472-0.07040.46610.0984-0.09960.0750.067-0.08110.28690.0895-0.08030.26470.0560.0738-41.023214.103192.7968
30.33540.03310.24540.4415-0.44052.33140.0463-0.0663-0.12180.0010.0328-0.03080.23410.0699-0.07920.10460.012-0.05240.06840.02750.2051-49.05799.716850.237
41.8266-0.2155-0.10651.67121.03542.81890.04270.1346-0.0332-0.13290.0696-0.01230.3675-0.1192-0.11220.1587-0.0214-0.05610.0328-0.02060.1986-53.884212.45912.7542
50.66910.41871.45391.15982.15139.62660.0196-0.0609-0.09590.0178-0.0212-0.06660.36480.1760.00160.13810.0343-0.02440.0722-0.02780.2039-44.551511.370621.3618
60.9451-0.0457-0.69040.84090.56651.88580.0362-0.133-0.080.11550.04830.07370.0665-0.0589-0.08450.0981-0.0078-0.00730.09690.0280.1677-53.21821.772959.7398
71.4473-0.2178-3.38620.39360.941112.61910.04680.0232-0.0184-0.07660.0469-0.0461-0.16930.1368-0.09370.1376-0.0047-0.01070.0998-0.01270.1929-49.45920.985318.6935
82.0302-0.2448-0.3932.5556-0.31842.1262-0.02280.2586-0.0579-0.29890.0296-0.07020.12470.0206-0.00670.1598-0.0002-0.00460.0838-0.06170.1325-46.848516.7421-6.4361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 135
2X-RAY DIFFRACTION2A136 - 258
3X-RAY DIFFRACTION3A259 - 325
4X-RAY DIFFRACTION4B1 - 26
5X-RAY DIFFRACTION5B27 - 60
6X-RAY DIFFRACTION6B61 - 97
7X-RAY DIFFRACTION7B98 - 126
8X-RAY DIFFRACTION8B127 - 173

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