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

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Basic information

Entry
Database: PDB / ID: 6bkn
TitleCrystal structure of the A/Wyoming/3/2003 (H3N2) influenza virus hemagglutinin 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 / 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
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 / 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 / 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 2.2Nov 20, 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)59,0879
Polymers55,9152
Non-polymers3,1727
Water7,909439
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,47621
Polymers107,6233
Non-polymers8,85218
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)177,26027
Polymers167,7446
Non-polymers9,51621
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 area44830 Å2
ΔGint10 kcal/mol
Surface area59660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.334, 100.333, 385.597
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-487-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 35874.480 Da / Num. of mol.: 1 / Mutation: 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, 7 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)-[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.: 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


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, 439 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 3.34 Å3/Da / Density % sol: 63.17 %
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: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 63929 / % possible obs: 98.7 % / Redundancy: 17.5 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 43.3
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 16 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5808 / CC1/2: 0.93 / Rpim(I) all: 0.24 / Rsym value: 0.95 / % possible all: 99.5

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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: 1.85→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.143 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18477 3221 5 %RANDOM
Rwork0.16676 ---
obs0.16766 60707 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å2-0 Å2
2--0.83 Å2-0 Å2
3----2.69 Å2
Refinement stepCycle: 1 / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 209 439 4517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194239
X-RAY DIFFRACTIONr_bond_other_d0.0020.023780
X-RAY DIFFRACTIONr_angle_refined_deg1.47425784
X-RAY DIFFRACTIONr_angle_other_deg0.93338853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89124.596198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86415697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.871526
X-RAY DIFFRACTIONr_chiral_restr0.0860.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
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_it1.0242.2131978
X-RAY DIFFRACTIONr_mcbond_other1.0242.2131977
X-RAY DIFFRACTIONr_mcangle_it1.6613.3132474
X-RAY DIFFRACTIONr_mcangle_other1.663.3122475
X-RAY DIFFRACTIONr_scbond_it1.7392.7572261
X-RAY DIFFRACTIONr_scbond_other1.7392.7592262
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9294.0773301
X-RAY DIFFRACTIONr_long_range_B_refined6.45146.31717350
X-RAY DIFFRACTIONr_long_range_B_other6.12945.47116976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.845→1.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 237 -
Rwork0.246 4333 -
obs--95.65 %
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)
10.374-0.02820.20960.2449-0.13661.74990.06940.0997-0.0226-0.09120.04290.12220.0747-0.2336-0.11230.0546-0.0129-0.05670.10060.03380.145629.3425-35.2713-63.1379
22.0492-0.06890.01671.86430.05392.29770.11650.43360.0678-0.368-0.03440.16780.0094-0.1868-0.08210.18680.0287-0.09970.29690.07250.08130.1578-27.1369-95.7315
38.1107-0.42010.986424.71664.70385.38230.12750.21930.0847-0.32280.0712-0.5565-0.18350.2508-0.19870.1223-0.01970.00820.2420.09860.121641.8579-19.4039-90.5616
42.2099-0.7541-0.19251.2448-0.00711.56770.1720.39210.0183-0.380.00240.1045-0.0543-0.0747-0.17440.17670.0014-0.070.25020.05180.07234.654-28.9535-90.4378
50.3034-0.03460.51050.3052-0.09221.63020.0442-0.0014-0.0165-0.01760.03190.10910.0522-0.1848-0.07620.0329-0.0188-0.03220.08220.03250.155932.4623-36.5255-50.4492
613.87764.7755-1.82314.08560.01682.4634-0.0253-0.1482-0.14380.08670.0551-0.09670.22850.0474-0.02990.13220.0069-0.00140.12150.01390.133541.0332-40.9097-13.6619
70.60380.7611-1.81211.9049-2.7417.95490.0427-0.01990.05080.0510.0150.1368-0.1822-0.3295-0.05760.0549-0.0090.02340.15120.02830.163731.0661-33.845-14.5085
81.2583-0.4589-1.07390.6277-0.04122.87730.00070.0008-0.04150.09660.05220.0812-0.0253-0.2829-0.05290.1225-0.0049-0.01410.14440.02170.198736.4491-30.8855-54.9494
90.5573-0.1663-1.77960.30630.51928.84850.0349-0.007-0.0237-0.0073-0.00120.02640.01940.0333-0.03380.0782-0.0184-0.00670.0880.0020.160445.739-34.1459-39.7663
102.42340.32930.69112.3520.732.7518-0.0091-0.19830.10380.18430.02030.12220.0187-0.0144-0.01120.0645-0.0290.05360.09380.01540.102936.791-30.68624.6302
1124.6315-5.25310.4841.6613-0.86449.1455-0.1627-1.721-0.2590.18490.4511-0.11730.540.3196-0.28850.5337-0.0209-0.10370.81720.22130.463845.9092-35.075514.6918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 141
2X-RAY DIFFRACTION2A142 - 200
3X-RAY DIFFRACTION3A201 - 214
4X-RAY DIFFRACTION4A215 - 258
5X-RAY DIFFRACTION5A259 - 325
6X-RAY DIFFRACTION6B1 - 17
7X-RAY DIFFRACTION7B18 - 53
8X-RAY DIFFRACTION8B54 - 71
9X-RAY DIFFRACTION9B72 - 123
10X-RAY DIFFRACTION10B124 - 168
11X-RAY DIFFRACTION11B169 - 173

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