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

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Basic information

Entry
Database: PDB / ID: 6aor
TitleCrystal structure of the A/Brisbane/10/2007 (H3N2) influenza virus hemagglutinin apo form
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / Influenza A virus / hemagglutinin / mutant / receptor binding / antigenicity
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 / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: PLoS Pathog. / Year: 2017
Title: A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine.
Authors: Wu, N.C. / Zost, S.J. / Thompson, A.J. / Oyen, D. / Nycholat, C.M. / McBride, R. / Paulson, J.C. / Hensley, S.E. / Wilson, I.A.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 6, 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)58,74110
Polymers55,8762
Non-polymers2,8668
Water8,863492
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)176,22430
Polymers167,6276
Non-polymers8,59724
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 area42580 Å2
ΔGint2 kcal/mol
Surface area60840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.556, 100.556, 384.183
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-530-

HOH

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Components

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Hemagglutinin ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin HA1 chain


Mass: 35922.480 Da / Num. of mol.: 1
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, UniProt: B2VNK2*PLUS
#2: Protein Hemagglutinin HA2 chain


Mass: 19953.174 Da / Num. of mol.: 1
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: A8W891, UniProt: C3PR70*PLUS

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Sugars , 3 types, 8 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)-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: 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.: 5
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, 492 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 63.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M bicine pH 9 and 41% 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: 1.7→50 Å / Num. obs: 81614 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.09 / Net I/σ(I): 51.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 8029 / CC1/2: 0.93 / Rpim(I) all: 0.21 / Rsym value: 0.87 / % possible all: 100

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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: 1.7→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.675 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19624 4100 5 %RANDOM
Rwork0.16888 ---
obs0.17024 77511 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.184 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.33 Å20 Å2
2--0.65 Å20 Å2
3----2.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 187 492 4546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194201
X-RAY DIFFRACTIONr_bond_other_d0.0020.023732
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9915728
X-RAY DIFFRACTIONr_angle_other_deg0.94238736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83624.75200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39615687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8591525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
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_it0.811.8091974
X-RAY DIFFRACTIONr_mcbond_other0.811.8091973
X-RAY DIFFRACTIONr_mcangle_it1.3182.7092468
X-RAY DIFFRACTIONr_mcangle_other1.3172.7092469
X-RAY DIFFRACTIONr_scbond_it1.6722.2882227
X-RAY DIFFRACTIONr_scbond_other1.6722.292228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8133.3783253
X-RAY DIFFRACTIONr_long_range_B_refined7.78738.77917272
X-RAY DIFFRACTIONr_long_range_B_other7.09737.50616766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.707→1.751 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 305 -
Rwork0.238 5586 -
obs--98.94 %
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)
10.4717-0.2586-1.08241.07761.27553.8571-0.02280.1005-0.08310.0254-0.06820.09620.2277-0.34440.0910.0855-0.0162-0.03330.0763-0.02120.1312-57.301212.969320.1065
20.40030.00510.19580.67190.29032.21860.0565-0.1732-0.15210.23880.0979-0.09270.32530.1102-0.15450.15950.0382-0.08010.10830.05220.1069-41.97486.770772.8985
32.19060.06260.41851.33941.14672.49290.0221-0.576-0.29340.60130.1198-0.22260.63270.187-0.14190.46830.0975-0.14180.37540.09250.0992-37.36697.536595.8485
43.52080.6155-2.05391.6026-0.46344.9674-0.0564-0.47940.01230.36580.1533-0.09440.16040.0009-0.09690.3210.0632-0.10190.24960.03070.0536-41.175614.955794.666
513.09738.2905-1.03611.051-4.0443.96530.1946-0.64720.25330.2913-0.1555-0.0311-0.37260.1798-0.03910.27440.0453-0.11170.2312-0.07840.1267-36.580926.580890.5148
62.574-0.3289-0.06891.04560.22291.12780.0467-0.4775-0.04380.40690.1061-0.0420.03240.1311-0.15270.30890.0353-0.07450.25730.03280.0702-42.446415.717990.4375
70.9123-0.25450.50540.7708-0.55311.78520.0399-0.0397-0.090.00340.0148-0.03770.17840.0702-0.05470.11020.0128-0.04180.06950.01590.1269-46.50049.584955.323
83.69970.79251.77261.94630.836910.87810.00260.1079-0.1901-0.07280.04190.10120.4026-0.401-0.04450.1244-0.0127-0.00450.047-0.00520.1321-56.209711.678523.8301
92.1314-1.7498-0.312411.74841.24472.26390.03330.1165-0.0067-0.14960.02020.1360.064-0.2292-0.05350.1151-0.0074-0.01250.1111-0.00580.1143-56.163615.158113.4598
100.69980.74381.32691.40722.51327.04720.02330.0001-0.10610.00330.0379-0.0940.22450.2811-0.06130.13390.0265-0.01440.067-0.0350.1319-45.25639.898114.3009
112.1359-0.69950.14180.8752-3.628519.8911-0.2028-0.12440.02230.2116-0.0707-0.0667-0.77480.64220.27350.2168-0.0032-0.05790.206-0.02030.259-41.386915.759441.537
126.971-0.4909-3.50962.82210.51674.6276-0.0704-0.025-0.24030.01530.06750.00890.26220.0510.00290.14850.0056-0.03840.10080.01770.1232-47.371116.399762.4961
131.0161-0.14-1.02390.9430.83686.13590.0171-0.1082-0.0530.08010.0390.06830.1195-0.0459-0.05610.0937-0.0035-0.00140.08950.01980.1153-55.342924.113357.8203
141.47250.1197-3.27680.43680.011312.49480.04460.00190.0286-0.04750.0409-0.0358-0.25540.1466-0.08560.1115-0.0074-0.00860.0715-0.01330.1301-49.009320.862718.3505
151.9166-0.1566-0.04041.9937-0.78132.24480.01380.2022-0.0343-0.1615-0.0086-0.10480.0390.0137-0.00520.12620.00510.01190.0545-0.04160.0998-45.220516.2985-5.3146
1622.5585-19.8752-1.260317.83952.43645.53531.69441.32190.0827-1.4184-1.4716-0.07510.1846-1.4444-0.22280.66090.0543-0.3730.49430.07090.6507-53.543822.312-14.8391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 37
2X-RAY DIFFRACTION2A38 - 131
3X-RAY DIFFRACTION3A132 - 171
4X-RAY DIFFRACTION4A172 - 199
5X-RAY DIFFRACTION5A200 - 212
6X-RAY DIFFRACTION6A213 - 258
7X-RAY DIFFRACTION7A259 - 314
8X-RAY DIFFRACTION8A315 - 325
9X-RAY DIFFRACTION9B1 - 17
10X-RAY DIFFRACTION10B18 - 53
11X-RAY DIFFRACTION11B54 - 60
12X-RAY DIFFRACTION12B61 - 71
13X-RAY DIFFRACTION13B72 - 98
14X-RAY DIFFRACTION14B99 - 125
15X-RAY DIFFRACTION15B126 - 168
16X-RAY DIFFRACTION16B169 - 173

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