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- PDB-6bks: Crystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus ... -

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Basic information

Entry
Database: PDB / ID: 6bks
TitleCrystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin D190E mutant 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 / 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 / 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
N-acetyl-alpha-neuraminic acid / 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: 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _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
Revision 2.2Oct 30, 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
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,46911
Polymers55,9292
Non-polymers3,5409
Water9,422523
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,62327
Polymers107,6663
Non-polymers9,95724
Water543
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
2
B: Hemagglutinin
hetero molecules

B: Hemagglutinin
hetero molecules

B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7846
Polymers60,1213
Non-polymers6643
Water543
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
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)178,40733
Polymers167,7866
Non-polymers10,62127
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 area46160 Å2
ΔGint17 kcal/mol
Surface area59680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.612, 100.612, 385.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-520-

HOH

21B-535-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 35888.504 Da / Num. of mol.: 1 / Mutation: D190E, S219F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A4GYF9
#2: Protein Hemagglutinin


Mass: 20040.211 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: B4UPH9

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Sugars , 5 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.: 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
#4: 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
#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.: 4
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
#7: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 523 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine pH 9 and 42% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 70033 / % possible obs: 99.6 % / Redundancy: 17.1 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.08 / Net I/σ(I): 39.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6052 / CC1/2: 0.95 / Rpim(I) all: 0.12 / Rsym value: 0.45 / % possible all: 95.5

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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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.4 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18896 3484 5 %RANDOM
Rwork0.16468 ---
obs0.1659 66368 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.28 Å20 Å2
2--0.57 Å20 Å2
3----1.84 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 233 523 4626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194265
X-RAY DIFFRACTIONr_bond_other_d0.0020.023794
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0065823
X-RAY DIFFRACTIONr_angle_other_deg0.9838888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3424.67197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26515695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.661525
X-RAY DIFFRACTIONr_chiral_restr0.0930.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02828
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_it0.7851.611984
X-RAY DIFFRACTIONr_mcbond_other0.7851.611983
X-RAY DIFFRACTIONr_mcangle_it1.3412.4092484
X-RAY DIFFRACTIONr_mcangle_other1.3412.412485
X-RAY DIFFRACTIONr_scbond_it1.5862.1682281
X-RAY DIFFRACTIONr_scbond_other1.5852.1682281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7643.2053332
X-RAY DIFFRACTIONr_long_range_B_refined6.48635.30317587
X-RAY DIFFRACTIONr_long_range_B_other5.84734.11117048
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
Rfree0.291 232 -
Rwork0.281 4552 -
obs--93.07 %
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)
10.34610.0554-0.31110.50250.35392.9474-0.0356-0.0165-0.0532-0.01790.02230.06990.2797-0.22480.01330.0827-0.0282-0.00670.06860.03320.080838.0181-42.401-26.0625
20.63370.0686-0.7540.437-0.18953.29450.00140.202-0.0385-0.13430.10120.14630.1682-0.2658-0.10260.1019-0.0302-0.09340.19420.03010.091824.638-35.6946-73.7487
30.9887-0.0644-0.40750.7019-0.04940.96040.04570.36790.0777-0.28570.05050.1167-0.0371-0.2884-0.09620.21940.0005-0.08880.32090.07490.056927.1976-27.1188-90.5839
42.5912-0.7172-1.21263.32293.37636.44390.20410.33460.0763-0.47030.0654-0.1244-0.25360.0787-0.26950.2281-0.0022-0.05320.25360.08070.066735.0297-28.4368-95.2873
51.7947-0.5299-0.03941.42410.12491.4940.11510.33220.1067-0.3390.03270.0466-0.0909-0.0505-0.14780.2171-0.0132-0.04360.2950.05830.0436.4839-26.8532-90.4908
60.2196-0.06740.43430.1287-0.14861.82680.03710.0051-0.0122-0.02030.02210.07580.038-0.1595-0.05930.0755-0.016-0.03020.11070.02790.079732.426-36.2742-51.0611
711.72033.7865-1.76432.50380.05012.04190.0154-0.1582-0.09190.08980.0273-0.02370.2016-0.0084-0.04270.1217-0.0003-0.00490.09430.02140.086841.0517-40.941-13.6455
80.46540.4144-1.03781.4202-1.99826.4060.00240.00080.03550.0120.00520.0906-0.1327-0.2533-0.00750.0567-0.00250.01430.12490.02010.105831.5114-33.4106-16.8267
92.9705-1.7455-2.66693.0751.96673.6957-0.0262-0.05590.00120.16750.06320.07580.142-0.1829-0.0370.1031-0.0033-0.03060.13570.01740.081537.0568-31.7631-59.492
100.4021-0.1184-1.3220.23980.32366.76050.0336-0.0043-0.0155-0.00560.01470.02260.03790.0422-0.04830.0733-0.0115-0.010.08150.00340.102445.8166-34.2131-39.7289
112.110.67340.68641.92220.60722.1847-0.0162-0.19290.13910.11440.03020.125-0.0224-0.0458-0.0140.0843-0.01740.03890.10570.00740.039936.7518-30.59054.6502
1226.3306-8.73767.67534.690.0696.0609-0.3864-1.5876-0.34260.66430.8021-0.10280.6759-0.0772-0.41570.3058-0.108-0.13730.71370.32580.361746.1211-35.035114.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 48
2X-RAY DIFFRACTION2A49 - 101
3X-RAY DIFFRACTION3A102 - 172
4X-RAY DIFFRACTION4A173 - 201
5X-RAY DIFFRACTION5A202 - 257
6X-RAY DIFFRACTION6A258 - 325
7X-RAY DIFFRACTION7B1 - 17
8X-RAY DIFFRACTION8B18 - 57
9X-RAY DIFFRACTION9B58 - 71
10X-RAY DIFFRACTION10B72 - 123
11X-RAY DIFFRACTION11B124 - 168
12X-RAY DIFFRACTION12B169 - 173

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