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

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Basic information

Entry
Database: PDB / ID: 6bko
TitleCrystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin D190E mutant apo form
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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
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

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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)59,16010
Polymers55,9292
Non-polymers3,2318
Water8,611478
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,69524
Polymers107,6663
Non-polymers9,02921
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)177,47930
Polymers167,7866
Non-polymers9,69324
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 area44990 Å2
ΔGint12 kcal/mol
Surface area59590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.410, 100.410, 384.444
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-508-

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 , 4 types, 8 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.: 2
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)-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.: 1
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
#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.: 1
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 / N-Acetylglucosamine


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

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Non-polymers , 1 types, 478 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 3.33 Å3/Da / Density % sol: 63.11 %
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: 1.85→50 Å / Num. obs: 64323 / % possible obs: 100 % / Redundancy: 18 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.08 / Net I/σ(I): 36.7
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 14 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5731 / CC1/2: 0.91 / Rpim(I) all: 0.17 / Rsym value: 0.65 / % possible all: 99.6

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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: 1.85→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.423 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18784 3058 4.8 %RANDOM
Rwork0.16491 ---
obs0.16601 61142 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 212 478 4560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194235
X-RAY DIFFRACTIONr_bond_other_d0.0020.023783
X-RAY DIFFRACTIONr_angle_refined_deg1.5572.0015776
X-RAY DIFFRACTIONr_angle_other_deg0.95938859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.643196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29715698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2571525
X-RAY DIFFRACTIONr_chiral_restr0.090.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
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_it0.7711.6461976
X-RAY DIFFRACTIONr_mcbond_other0.7711.6461975
X-RAY DIFFRACTIONr_mcangle_it1.292.4642471
X-RAY DIFFRACTIONr_mcangle_other1.292.4642472
X-RAY DIFFRACTIONr_scbond_it1.5522.1622259
X-RAY DIFFRACTIONr_scbond_other1.5522.1642260
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6963.1973296
X-RAY DIFFRACTIONr_long_range_B_refined6.14535.56517439
X-RAY DIFFRACTIONr_long_range_B_other5.62734.54916975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 214 -
Rwork0.311 4434 -
obs--98.81 %
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)
10.38590.0413-0.24940.53130.28952.9232-0.028-0.0081-0.049-0.01060.01420.04680.2744-0.21330.01380.0773-0.02690.00260.06940.02990.094337.8601-42.3919-25.9626
20.57570.0094-0.56550.5351-0.25372.12760.030.25460.0391-0.14690.1170.15740.0281-0.3581-0.1470.0817-0.0175-0.07990.20090.05460.088326.1999-31.7472-77.5576
32.21330.4722-0.54511.7814-0.7341.8040.08210.33120.1411-0.3265-0.02340.2265-0.0039-0.3715-0.05870.17380.02-0.10060.33050.0840.094626.3552-26.2487-92.7937
42.0616-1.0819-0.72632.19173.04938.1480.18370.50890.1319-0.40260.0367-0.1529-0.240.1699-0.22050.2966-0.0192-0.04110.33060.02810.084936.819-33.0181-100.8779
56.3470.37880.380319.75452.70094.57930.1805-0.03040.16030.1302-0.1308-0.26-0.15720.0093-0.04970.1309-0.02050.00870.22120.08490.08741.5876-18.952-89.4834
61.9928-0.7879-0.31161.46340.09911.71610.12460.33390.0573-0.3420.07970.0837-0.0574-0.1-0.20430.1843-0.0246-0.06760.27290.05290.060634.644-29.0107-90.2929
70.3146-0.06670.5870.1735-0.08021.64850.0285-0.0003-0.0054-0.0090.01210.07550.0411-0.1313-0.04060.058-0.0171-0.02290.09080.02380.099532.4971-36.5448-50.3701
812.33484.2257-1.63532.9902-0.09712.08190.0111-0.2157-0.13280.09330.0038-0.06010.2003-0.0028-0.01490.11770.0061-0.00260.09760.01540.094241.0173-40.8946-13.5887
90.51080.4641-1.08511.4091-2.07656.97190.0053-0.00360.02890.0180.00480.0796-0.1529-0.2627-0.01010.0593-0.0020.0150.12460.01780.11931.4639-33.3929-16.7871
103.2479-2.585-3.00363.19262.30713.5017-0.028-0.0209-0.01030.16990.00710.08210.1908-0.23720.02090.1316-0.02-0.01980.16180.01040.156736.9603-31.7313-59.4189
110.4497-0.1317-1.41330.25010.35987.11290.0206-0.0053-0.02220.001-0.00440.02080.01720.0205-0.01620.0732-0.0133-0.00780.07840.00240.118845.7454-34.1436-39.6853
122.09330.62770.44781.84340.63822.3971-0.0212-0.17440.10670.14470.01670.13740.00220.00010.00450.0775-0.01960.04040.09450.00870.043936.6834-30.78954.7645
1327.0155-7.82828.38813.76030.08846.8591-0.3166-1.6523-0.33670.57830.8-0.12880.73830.0239-0.48330.3882-0.0908-0.12880.63490.24310.390645.9604-35.029914.7051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 48
2X-RAY DIFFRACTION2A49 - 134
3X-RAY DIFFRACTION3A135 - 179
4X-RAY DIFFRACTION4A180 - 201
5X-RAY DIFFRACTION5A202 - 214
6X-RAY DIFFRACTION6A215 - 258
7X-RAY DIFFRACTION7A259 - 325
8X-RAY DIFFRACTION8B1 - 17
9X-RAY DIFFRACTION9B18 - 57
10X-RAY DIFFRACTION10B58 - 71
11X-RAY DIFFRACTION11B72 - 123
12X-RAY DIFFRACTION12B124 - 168
13X-RAY DIFFRACTION13B169 - 173

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