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

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Basic information

Entry
Database: PDB / ID: 6nsc
TitleCrystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin G186V/L194P mutant apo form
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


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 / 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
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 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 2.2Nov 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)58,6458
Polymers55,8732
Non-polymers2,7736
Water4,324240
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)175,93624
Polymers167,6186
Non-polymers8,31818
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 area42290 Å2
ΔGint-12 kcal/mol
Surface area61930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.601, 100.601, 384.460
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: 35763.336 Da / Num. of mol.: 1 / Fragment: residues 27-345 / Mutation: G186V, L194P
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: A8W893
#2: Protein Hemagglutinin HA2 chain


Mass: 20109.355 Da / Num. of mol.: 1 / Fragment: residues 330-505
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

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Sugars , 4 types, 6 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}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.: 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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, 240 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CAPS pH 10.5 and 29% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 36162 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 36 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.1 / Net I/σ(I): 29.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 17.1 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3556 / CC1/2: 0.92 / Rpim(I) all: 0.22 / Rsym value: 0.89 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000712data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOQ

6aoq


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.513 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.185 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22844 1743 4.8 %RANDOM
Rwork0.19758 ---
obs0.19906 34376 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 64.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.71 Å20 Å2
2--1.43 Å20 Å2
3----4.64 Å2
Refinement stepCycle: 1 / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 183 240 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194189
X-RAY DIFFRACTIONr_bond_other_d0.0020.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9915711
X-RAY DIFFRACTIONr_angle_other_deg0.9538690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82124.85200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6391524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024573
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02813
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_it1.0113.3291970
X-RAY DIFFRACTIONr_mcbond_other1.0123.331969
X-RAY DIFFRACTIONr_mcangle_it1.7564.992462
X-RAY DIFFRACTIONr_mcangle_other1.7564.9882463
X-RAY DIFFRACTIONr_scbond_it1.7324.0132219
X-RAY DIFFRACTIONr_scbond_other1.7324.0122220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0965.9953244
X-RAY DIFFRACTIONr_long_range_B_refined6.84666.81816397
X-RAY DIFFRACTIONr_long_range_B_other6.82966.61616250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 129 -
Rwork0.345 2475 -
obs--98.52 %
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)
10.5306-0.03890.07910.4885-0.37472.16960.0745-0.2509-0.22260.15210.064-0.03990.25160.1001-0.13850.17370.0183-0.08640.13990.07670.2412-44.51687.200365.9617
20.0016-0.00250.00290.0045-0.00540.0073-0.0386-0.0244-0.03530.06580.06090.0348-0.0996-0.0535-0.02231.7010.05830.38471.73880.31.4528-37.068213.2385107.43
39.08233.1411-1.11735.7256-0.79355.67650.1107-0.8420.66740.36710.0887-0.5155-0.13850.2618-0.19940.34050.014-0.15620.3268-0.10820.2258-32.547118.173186.7199
45.58834.8734-1.05239.453-0.97910.203-0.60531.2212-0.89551.2210.3788-0.5160.036-0.20690.22651.8037-0.0617-0.39521.53030.08561.5239-48.490511.7409105.0902
55.6689-0.51122.18693.28370.82262.4082-0.0099-1.55350.33020.82420.0888-0.0138-0.1087-0.3298-0.07890.63170.0277-0.07090.7721-0.0890.1955-41.416318.256490.6522
60.5375-0.060.33320.7673-0.50962.45110.0685-0.0957-0.17120.07280.0701-0.11860.23990.1023-0.13870.13630.0147-0.06540.08670.02580.2539-47.9579.968250.2249
70.46110.1891-0.18490.8090.64683.25040.05680.0024-0.0736-0.01290.0355-0.06170.40370.2099-0.09220.1840.0226-0.04330.0455-0.04550.2666-47.958612.045217.3249
80.1707-0.1011-0.1660.24320.43833.62670.0198-0.0371-0.10230.0360.03490.03260.1099-0.1127-0.05470.1277-0.0152-0.01760.09320.01550.2437-51.603721.422944.0924
91.6507-0.2491-1.18563.0242-0.75563.3966-0.02540.291-0.0311-0.24250.0055-0.15490.13260.01330.01990.18830.00140.00390.1076-0.07860.2055-45.281116.5204-4.9986
1024.235-21.34687.131519.1337-6.64642.50251.08071.7602-0.7416-0.9451-1.03970.52080.3063-0.034-0.0410.9584-0.0655-0.31190.99-0.05790.6292-53.800422.1769-15.0437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 154
2X-RAY DIFFRACTION2A155 - 164
3X-RAY DIFFRACTION3A165 - 185
4X-RAY DIFFRACTION4A186 - 197
5X-RAY DIFFRACTION5A198 - 258
6X-RAY DIFFRACTION6A259 - 325
7X-RAY DIFFRACTION7B1 - 60
8X-RAY DIFFRACTION8B61 - 123
9X-RAY DIFFRACTION9B124 - 168
10X-RAY DIFFRACTION10B169 - 173

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