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- PDB-6ona: Crystal structure of Influenza hemagglutinin from strain A/Hickox... -

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Basic information

Entry
Database: PDB / ID: 6ona
TitleCrystal structure of Influenza hemagglutinin from strain A/Hickox/JY2/1940
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Inflenza hemagglutinin / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / 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
DI(HYDROXYETHYL)ETHER / Envelope glycoprotein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Sci Rep / Year: 2023
Title: Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Authors: Ghafoori, S.M. / Petersen, G.F. / Conrady, D.G. / Calhoun, B.M. / Stigliano, M.Z.Z. / Baydo, R.O. / Grice, R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Forwood, J.K.
History
DepositionApr 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1May 24, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,61832
Polymers182,1713
Non-polymers5,44629
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19720 Å2
ΔGint-40 kcal/mol
Surface area58400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.560, 102.250, 160.950
Angle α, β, γ (deg.)90.000, 91.070, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-792-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Hemagglutinin /


Mass: 60723.797 Da / Num. of mol.: 3 / Fragment: UNP residues 18-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hickox/1940 H1N1)
Strain: A/Hickox/1940 H1N1 / Gene: HA / Plasmid: InvbQ.18715.a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0HD60, UniProt: M1E1E4

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Sugars , 3 types, 15 molecules

#2: 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
#3: 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
#4: 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.: 11
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 , 3 types, 666 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 uL 9.5 mg/mL SEC-purified InvbQ.18715.a.KN11.PD38349 in 2 5 mM Tris, pH 8.5, 150 mM sodium chloride + 0.1 uL mother liquor (0.1 M sodium citrate, pH 5.5, 0.1 M magnesium chloride, 34% ...Details: 0.1 uL 9.5 mg/mL SEC-purified InvbQ.18715.a.KN11.PD38349 in 2 5 mM Tris, pH 8.5, 150 mM sodium chloride + 0.1 uL mother liquor (0.1 M sodium citrate, pH 5.5, 0.1 M magnesium chloride, 34% PEG400), flash-frozen, crystal ID 308018c7 data set les6-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→45.388 Å / Num. obs: 127783 / % possible obs: 99.9 % / Redundancy: 5.18 % / Biso Wilson estimate: 38.193 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 1.079 / Net I/σ(I): 12.85 / Num. measured all: 661978 / Scaling rejects: 75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-25.3010.8752.1394500.8060.97499.9
2-2.065.3030.6832.7191830.8520.76100
2.06-2.125.2950.5343.4289240.8930.59599.9
2.12-2.185.2840.4514.0687130.930.502100
2.18-2.255.2840.3614.9784030.9490.402100
2.25-2.335.2650.2925.9381620.9650.32599.9
2.33-2.425.2670.2576.7378420.9710.286100
2.42-2.525.2330.1998.2775370.9830.22199.9
2.52-2.635.2120.1639.8472710.9880.18199.9
2.63-2.765.1430.12611.7869920.9930.14199.9
2.76-2.915.0910.09814.5665260.9950.10999.8
2.91-3.085.0410.08317.0762570.9950.09399.7
3.08-3.34.9860.06521.0858610.9960.07399.6
3.3-3.564.9180.05224.8354760.9980.05999.5
3.56-3.94.9430.04329.3250000.9980.04899.4
3.9-4.364.9910.03832.3445800.9990.04399.7
4.36-5.035.1190.03335.0540390.9990.03699.9
5.03-6.175.1970.03135.2234120.9990.034100
6.17-8.725.1490.02936.2326580.9990.032100
8.72-45.3884.8840.02638.5914970.9980.02998.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3409refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MYA

6mya


Resolution: 1.95→45.388 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2048 1.6 %
Rwork0.193 125641 -
obs0.1936 127689 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.4 Å2 / Biso mean: 43.8077 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 1.95→45.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11173 0 344 654 12171
Biso mean--68.04 44.02 -
Num. residues----1444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99540.391100.338683388448100
1.9954-2.04530.35241350.309783718506100
2.0453-2.10060.27371380.276383228460100
2.1006-2.16240.31731360.254683488484100
2.1624-2.23220.25641210.243983758496100
2.2322-2.3120.25531060.225983798485100
2.312-2.40450.291580.221184058563100
2.4045-2.51390.24261390.217983308469100
2.5139-2.64650.27571540.214983378491100
2.6465-2.81230.24381430.207983268469100
2.8123-3.02940.24281660.204483568522100
3.0294-3.33410.24491460.194183778523100
3.3341-3.81640.21031440.1658363850799
3.8164-4.80740.17221190.135984488567100
4.8074-45.40060.17521330.168985668699100
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)
12.68290.13691.50140.1504-0.08820.70130.30170.5405-0.792-0.11760.02430.02220.20510.2533-0.33250.30890.0805-0.13010.3975-0.17920.602610.5169-47.956626.0108
23.5787-0.60880.34831.3157-0.45292.0043-0.0483-0.24450.16760.06580.0073-0.0671-0.09620.0670.04720.22350.067-0.10860.2737-0.12350.515747.7798-42.533449.1847
34.94250.98491.73060.24110.40840.67330.20870.635-0.1705-0.1856-0.14620.02850.09580.0693-0.0480.30330.1154-0.12720.4818-0.13120.601728.25-44.811731.1814
41.88350.31451.71960.72210.43372.6510.17310.259-0.2645-0.158-0.00650.0920.1410.0703-0.17430.22890.031-0.09120.2447-0.07370.4864-5.1393-40.123922.668
53.5486-1.12982.08290.5807-0.37712.8619-0.18420.26540.2451-0.6573-0.29040.4475-0.7241-0.35320.4250.80880.0768-0.50280.5991-0.17390.8911-29.68-39.2649-3.2908
62.72040.95432.01970.42860.45091.8026-0.30110.25060.3915-0.18940.04660.108-0.28070.11190.28950.23580.0271-0.06750.25130.01370.45786.478-10.19230.7828
72.80570.67861.11231.63670.45262.21250.07590.0087-0.3080.19330.0104-0.32090.07290.144-0.06240.2169-0.0198-0.07110.1742-0.01490.516940.4228-11.428960.4245
82.72920.91583.71830.36241.36535.3379-0.0352-0.0310.35470.023-0.02160.039-0.1715-0.08830.03270.17530.0041-0.00980.2011-0.01510.472918.4805-6.726846.0476
93.0571-0.40691.63671.0651-0.49741.7665-0.05170.15170.1067-0.20380.09170.3033-0.0733-0.1613-0.01940.20890.0179-0.07060.21160.00840.3857-12.2928-18.294723.8744
101.0839-0.4221.30980.343-0.1331.66150.0645-0.2995-0.1249-0.00710.02980.0850.0144-0.4891-0.10070.1889-0.0411-0.02520.42150.01710.5075-18.776-32.372348.2513
117.62053.11826.61461.38493.05856.88780.1065-0.75330.09330.3102-0.16220.3120.1499-0.55150.06230.2873-0.0575-0.03410.34670.01640.451311.3963-37.77774.1705
123.5277-0.14170.93571.918-0.20342.12830.0498-0.3643-0.19680.3601-0.1742-0.2725-0.13250.270.04390.2858-0.104-0.10370.37640.10420.40430.0849-38.783977.0266
134.7562-0.49151.80991.346-0.23321.71870.1462-0.0283-0.31420.0653-0.15590.07820.0180.16250.00160.2398-0.0712-0.03210.20660.05630.34514.4442-42.264568.5329
143.03860.21351.22770.48290.04561.13430.0985-0.0941-0.1235-0.007-0.00050.13260.0339-0.2746-0.09070.16680.0095-0.04020.2379-0.01160.4236-15.9162-33.202739.739
157.00823.01120.67013.6732-0.37492.4207-0.48241.8555-0.2853-0.6820.4814-0.2475-0.044-0.60170.01840.367-0.1005-0.11631.1069-0.12730.6841-47.0296-39.431819.3191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 80 )A2 - 80
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 254 )A81 - 254
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 284 )A255 - 284
4X-RAY DIFFRACTION4chain 'A' and (resid 285 through 461 )A285 - 461
5X-RAY DIFFRACTION5chain 'A' and (resid 462 through 488 )A462 - 488
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 80 )B2 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 254 )B81 - 254
8X-RAY DIFFRACTION8chain 'B' and (resid 255 through 284 )B255 - 284
9X-RAY DIFFRACTION9chain 'B' and (resid 285 through 491 )B285 - 491
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 55 )C2 - 55
11X-RAY DIFFRACTION11chain 'C' and (resid 56 through 88 )C56 - 88
12X-RAY DIFFRACTION12chain 'C' and (resid 89 through 236 )C89 - 236
13X-RAY DIFFRACTION13chain 'C' and (resid 237 through 288 )C237 - 288
14X-RAY DIFFRACTION14chain 'C' and (resid 289 through 455 )C289 - 455
15X-RAY DIFFRACTION15chain 'C' and (resid 456 through 491 )C456 - 491

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