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

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Basic information

Entry
Database: PDB / ID: 6nsa
TitleCrystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin in complex with 3'-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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / 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 / _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_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
Revision 2.2Oct 23, 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)60,76711
Polymers56,0102
Non-polymers4,7579
Water7,620423
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)182,30233
Polymers168,0306
Non-polymers14,27227
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 area48230 Å2
ΔGint119 kcal/mol
Surface area64060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.462, 101.462, 388.077
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 , 5 types, 9 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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 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
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+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.: 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, 423 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 3.43 Å3/Da / Density % sol: 64.16 %
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: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 56657 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.11 / Net I/σ(I): 33.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.5 % / Num. unique obs: 5556 / CC1/2: 0.86 / Rpim(I) all: 0.38 / Rsym value: 0.99 / % possible all: 99.4

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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: 1.95→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.827 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20757 2840 5 %RANDOM
Rwork0.17942 ---
obs0.18084 53635 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.319 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----3.57 Å2
Refinement stepCycle: 1 / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3852 0 316 423 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194397
X-RAY DIFFRACTIONr_bond_other_d0.0020.023880
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.0266027
X-RAY DIFFRACTIONr_angle_other_deg0.95539122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95424.902204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13315703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2641525
X-RAY DIFFRACTIONr_chiral_restr0.0820.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024725
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02834
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_it0.8972.2861997
X-RAY DIFFRACTIONr_mcbond_other0.8982.2841996
X-RAY DIFFRACTIONr_mcangle_it1.5023.4192510
X-RAY DIFFRACTIONr_mcangle_other1.5013.422511
X-RAY DIFFRACTIONr_scbond_it1.7193.2052400
X-RAY DIFFRACTIONr_scbond_other1.7163.2052400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0254.7633508
X-RAY DIFFRACTIONr_long_range_B_refined6.25950.13817755
X-RAY DIFFRACTIONr_long_range_B_other6.03449.4717391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 220 -
Rwork0.241 3915 -
obs--99.4 %
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)
10.5155-0.01840.51320.2972-0.21792.21840.08430.0884-0.0543-0.0974-0.00340.11880.1372-0.1131-0.08090.04880.009-0.05540.05210.01010.175729.7393-35.3538-62.9642
21.8175-0.01960.23621.7673-0.20921.74050.06430.50230.0783-0.3726-0.02410.07020.01010.0335-0.04020.12860.0213-0.05780.22990.04850.060733.5811-26.5611-92.1714
30.4943-0.00560.70290.50610.01721.38530.0879-0.0371-0.0771-0.006-0.00640.13030.1218-0.1525-0.08150.0345-0.0202-0.02870.04250.02880.189133.2339-38.3448-48.765
47.3089-2.98560.91692.41870.88821.45650.20071.25251.23760.1051-0.1217-0.65590.21540.5602-0.0790.4574-0.26190.01820.88190.26420.703447.2595-37.8032-15.7925
50.70990.6457-1.46670.8972-1.77499.55150.0797-0.0889-0.0090.002-0.08250.0816-0.1723-0.43250.00290.0755-0.01790.0360.14530.02960.169432.4317-35.9157-17.4054
60.41350.1885-0.40620.5988-0.14972.12320.06070.015-0.0678-0.0008-0.00650.06290.02910.0119-0.05420.044-0.0073-0.00870.0364-0.00460.176544.9952-34.6879-50.2466
73.0830.538-1.00513.04340.65616.19630.2401-0.50560.06520.2752-0.0803-0.0425-0.25050.3309-0.15990.0931-0.10090.04440.1945-0.00480.113938.9809-31.78843.1643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 141
2X-RAY DIFFRACTION2A142 - 264
3X-RAY DIFFRACTION3A265 - 325
4X-RAY DIFFRACTION4B5 - 9
5X-RAY DIFFRACTION5B10 - 60
6X-RAY DIFFRACTION6B61 - 114
7X-RAY DIFFRACTION7B115 - 173

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