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- PDB-6nsb: Crystal structure of the IVR-165 (H3N2) influenza virus hemagglut... -

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Basic information

Entry
Database: PDB / ID: 6nsb
TitleCrystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 6'-SLNLN
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN
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 / 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, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility.
Authors: Wu, N.C. / Lv, H. / Thompson, A.J. / Wu, D.C. / Ng, W.W.S. / Kadam, R.U. / Lin, C.W. / Nycholat, C.M. / McBride, R. / Liang, W. / Paulson, J.C. / Mok, C.K.P. / Wilson, I.A.
History
DepositionJan 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 18, 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: Atomic model / Data collection ...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 / 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 / _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 11, 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)59,95711
Polymers56,0102
Non-polymers3,9479
Water9,314517
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)179,87033
Polymers168,0306
Non-polymers11,84027
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area48520 Å2
ΔGint56 kcal/mol
Surface area60810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.123, 101.123, 387.229
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: 35856.465 Da / Num. of mol.: 1 / Fragment: residues 27-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0HR89
#2: Protein Hemagglutinin HA2 chain


Mass: 20153.393 Da / Num. of mol.: 1 / Fragment: residues 346-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: L0HR89

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Sugars , 4 types, 9 molecules

#3: 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.: 3
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
#4: 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: 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
#5: 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
#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.: 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 , 1 types, 517 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 44% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 76888 / % possible obs: 100 % / Redundancy: 37.7 % / Biso Wilson estimate: 25 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.13 / Net I/σ(I): 39
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6920 / CC1/2: 0.92 / Rpim(I) all: 0.23 / Rsym value: 1.33 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
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: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.824 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18686 3825 5 %RANDOM
Rwork0.16484 ---
obs0.16594 73049 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.3 Å20 Å2
2--0.6 Å20 Å2
3----1.93 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 261 518 4658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194364
X-RAY DIFFRACTIONr_bond_other_d0.0020.023865
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0095968
X-RAY DIFFRACTIONr_angle_other_deg0.94939064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44524.689209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4041528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
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_it0.8721.8942004
X-RAY DIFFRACTIONr_mcbond_other0.8721.8942003
X-RAY DIFFRACTIONr_mcangle_it1.4122.8362515
X-RAY DIFFRACTIONr_mcangle_other1.4112.8362516
X-RAY DIFFRACTIONr_scbond_it1.7192.5862360
X-RAY DIFFRACTIONr_scbond_other1.7192.5862360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9733.8283441
X-RAY DIFFRACTIONr_long_range_B_refined6.5641.80417784
X-RAY DIFFRACTIONr_long_range_B_other6.14340.66617286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.753→1.799 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 281 -
Rwork0.282 5248 -
obs--98.24 %
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)
10.3684-0.050.34580.253-0.08441.47850.07750.0998-0.0352-0.11860.00540.11290.0849-0.1186-0.08280.087-0.0101-0.05720.09380.01950.09530.1578-35.4292-60.4083
22.15160.65590.36452.4475-0.20691.94960.05020.45650.1246-0.4731-0.06280.16520.0532-0.15290.01260.26460.0505-0.09930.35180.05090.055426.9291-25.9616-93.1109
37.1946-3.73671.53595.21660.025810.36310.23310.8321-0.0707-0.8992-0.1468-0.4009-0.0610.2733-0.08620.4473-0.00410.02430.3953-0.02270.087637.5934-34.0089-102.879
46.163-0.84440.508417.75912.41154.87980.0684-0.01220.13320.14570.053-0.342-0.06880.1603-0.12140.171-0.0262-0.00710.28320.09240.103441.9589-18.8125-89.5991
51.2413-0.33630.15961.20810.17840.95520.09050.41180.0132-0.3828-0.00280.04710.0034-0.0173-0.08780.25190.0068-0.05940.2920.02620.025634.9227-29.6814-90.7828
61.4669-0.2019-0.17731.8231-0.26652.10270.00560.1132-0.0275-0.11590.01670.1144-0.034-0.1815-0.02220.0925-0.0013-0.08350.13490.0270.110826.1735-31.837-64.2142
70.44120.06090.69670.56050.01932.34620.0623-0.0071-0.0327-0.01560.02050.11640.1265-0.1687-0.08280.0811-0.0231-0.02670.09090.02340.11735.6474-38.693-45.1736
81.4916-0.4053-1.58330.5780.54393.9320.0451-0.1123-0.01130.0090.00350.00190.2194-0.0804-0.04860.0885-0.05690.01920.09450.03480.104237.0737-40.2026-11.5739
91.64571.8398-4.2273.1237-5.593814.96940.0983-0.08080.05250.0567-0.01460.0606-0.2614-0.3069-0.08370.0728-0.00940.01970.15270.01380.160230.7427-33.2625-14.0039
100.1956-0.2336-0.13640.6787-0.56712.1914-0.03250.0491-0.12370.08620.06680.1848-0.1404-0.2696-0.03430.11250.0043-0.00260.13240.0330.129236.3611-30.5775-51.9398
110.4927-0.1208-1.31020.30930.42076.95120.0560.0039-0.01510.0076-0.00030.03170.0097-0.029-0.05570.0919-0.0229-0.00220.08630.00130.139245.7305-34.0689-38.4513
122.4611-0.02650.49412.00580.65522.5933-0.0169-0.2180.07880.18850.01320.10690.0204-0.15910.00370.0746-0.02830.04520.13030.00540.074936.9773-31.30515.16
1325.483-10.24874.69824.4658-0.23618.8338-0.7644-1.7689-0.43350.48840.92340.16530.7820.6002-0.1590.342-0.0728-0.13940.70740.33950.520446.3899-35.523514.6691
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 130
2X-RAY DIFFRACTION2A131 - 181
3X-RAY DIFFRACTION3A182 - 201
4X-RAY DIFFRACTION4A202 - 214
5X-RAY DIFFRACTION5A215 - 258
6X-RAY DIFFRACTION6A259 - 279
7X-RAY DIFFRACTION7A280 - 325
8X-RAY DIFFRACTION8B1 - 28
9X-RAY DIFFRACTION9B29 - 50
10X-RAY DIFFRACTION10B51 - 71
11X-RAY DIFFRACTION11B72 - 125
12X-RAY DIFFRACTION12B126 - 168
13X-RAY DIFFRACTION13B169 - 173

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