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- PDB-6n08: Crystal structure of hemagglutinin from influenza virus A/Netherl... -

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Basic information

Entry
Database: PDB / ID: 6n08
TitleCrystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / hemagglutinin influenza crystal structure / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / 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 (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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.916 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: to be published
Title: Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)
Authors: Dai, Y.N. / Fremont, D.H.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)174,02720
Polymers167,3833
Non-polymers6,64417
Water18,6461035
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.990, 188.770, 108.760
Angle α, β, γ (deg.)90.000, 109.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1031-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 295 or resid 297 through 706 or resid 708 through 709))
21(chain B and (resid 8 through 295 or resid 297 through 708 or resid 702 through 704))
31(chain C and (resid 8 through 295 or resid 297 through 711 or resid 705 through 702))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 295 or resid 297 through 706 or resid 708 through 709))A8 - 295
121(chain A and (resid 8 through 295 or resid 297 through 706 or resid 708 through 709))A297 - 706
131(chain A and (resid 8 through 295 or resid 297 through 706 or resid 708 through 709))A708 - 709
211(chain B and (resid 8 through 295 or resid 297 through 708 or resid 702 through 704))B8 - 295
221(chain B and (resid 8 through 295 or resid 297 through 708 or resid 702 through 704))B297 - 708
231(chain B and (resid 8 through 295 or resid 297 through 708 or resid 702 through 704))B702 - 704
311(chain C and (resid 8 through 295 or resid 297 through 711 or resid 705 through 702))C8 - 295
321(chain C and (resid 8 through 295 or resid 297 through 711 or resid 705 through 702))C297 - 711
331(chain C and (resid 8 through 295 or resid 297 through 711 or resid 705 through 702))C705 - 702

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Components

#1: Protein Hemagglutinin


Mass: 55794.266 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Netherlands/209/1980(H3N2))
Strain: A/Netherlands/209/1980(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: H9XIV6
#2: 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.: 7
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
#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.: 4
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: 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.: 6
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 5.83 Å3/Da / Density % sol: 78.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Oct 2, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.9→46.344 Å / Num. obs: 292124 / % possible obs: 97.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.994 / Net I/σ(I): 5.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 0.1 / Num. unique obs: 14353 / CC1/2: 0.264 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP5

2yp5


Resolution: 1.916→46.344 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74
RfactorNum. reflection% reflection
Rfree0.252 12929 4.92 %
Rwork0.2239 --
obs0.2253 262526 89.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.46 Å2 / Biso mean: 47.3988 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 1.916→46.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11559 0 436 1035 13030
Biso mean--71.02 47.49 -
Num. residues----1464
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7342X-RAY DIFFRACTION7.984TORSIONAL
12B7342X-RAY DIFFRACTION7.984TORSIONAL
13C7342X-RAY DIFFRACTION7.984TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9155-1.93730.43061600.37072813297331
1.9373-1.96010.34221120.32161849196120
1.9601-1.9840.352440.3324709495351
1.984-2.00910.38033900.35257299768979
2.0091-2.03550.35144060.35348426883291
2.0355-2.06340.3784470.34428897934496
2.0634-2.09290.3684650.3578963942897
2.0929-2.12410.35134980.32559028952698
2.1241-2.15730.34494450.31889102954798
2.1573-2.19270.34544300.31119058948898
2.1927-2.23050.34794740.30299054952898
2.2305-2.27110.36974420.30739051949397
2.2711-2.31470.34434420.3099032947497
2.3147-2.3620.31534430.27939100954398
2.362-2.41330.31264660.26829021948798
2.4133-2.46950.30375260.26729063958998
2.4695-2.53120.29644520.25819041949398
2.5312-2.59970.28324870.24289037952498
2.5997-2.67620.25954730.23379016948997
2.6762-2.76250.26284670.23959041950897
2.7625-2.86120.25824990.22858992949197
2.8612-2.97580.27914980.23298957945597
2.9758-3.11120.25714280.21269048947697
3.1112-3.27520.24374820.20118957943997
3.2752-3.48030.22484880.19718927941596
3.4803-3.74890.21784610.18448943940496
3.7489-4.1260.20464430.17538896933996
4.126-4.72250.1724730.15198856932995
4.7225-5.94790.18124510.16998834928595
5.9479-46.35760.21684370.20588587902491
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)
11.608-2.1284-1.74663.09552.47622.0659-0.3242-0.3227-0.16720.44240.21090.07370.3590.2470.08470.50380.12070.05240.33410.07340.24832.927234.561356.8678
21.7376-0.29290.22852.26920.40912.2912-0.00640.34290.056-0.663-0.1262-0.31610.13710.1870.12420.59550.11730.14190.25180.09140.350450.947813.879420.6459
31.9716-1.119-1.82181.33111.10741.8102-0.2219-0.236-0.11630.38860.11770.10540.26430.12140.09980.35970.07590.01490.29310.04130.186725.232644.421158.3486
46.55421.05710.10152.3808-1.32674.6707-0.2289-0.4368-0.00970.64270.14820.48690.0536-0.24170.13030.54970.05060.23250.31790.01210.3295-3.642562.251683.3199
53.9314-2.1045-2.43691.95821.32661.89520.2861-0.13260.6231-0.38630.1233-0.5377-0.33870.2703-0.42910.4656-0.08840.13040.2364-0.05980.405330.235774.08248.9063
62.2686-0.8659-0.36631.52160.19711.33850.2036-0.02140.0855-0.5043-0.0207-0.8508-0.00930.4675-0.16280.45290.00290.27210.44010.03590.739369.034143.752622.4937
72.1012-2.2725-2.45452.87882.82423.35070.1685-0.15310.3189-0.21030.0665-0.3289-0.26830.2345-0.23360.3601-0.05450.06350.2052-0.00540.285428.625567.204550.3749
83.5366-0.3337-1.4314.40281.60455.4941-0.0266-0.6130.37070.48180.11630.1492-0.25070.1553-0.10150.4121-0.04560.06140.258-0.11250.28557.007583.35378.8424
91.5762-0.7138-1.94531.31531.04083.00650.07290.429-0.2061-0.1697-0.30190.32450.063-0.42370.24250.21570.0058-0.06550.3339-0.04780.32684.789952.439539.7902
102.0115-0.2018-1.36651.49820.49782.66880.1680.2372-0.0525-0.6054-0.1969-0.23140.04320.0210.03060.79810.18040.10730.39160.05030.244942.015938.79410.7534
113.7077-2.7305-2.79942.54271.69922.21050.12810.3225-0.0092-0.17-0.1630.13360.0271-0.27950.03150.1843-0.0139-0.04990.2352-0.03620.233111.142555.044642.3053
124.9099-2.2895-0.71535.28671.86925.67960.0231-0.15210.22210.3790.12680.3852-0.4098-0.4053-0.1360.1960.00210.06080.2048-0.01630.3861-11.656676.43865.8368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 79 )A8 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 265 )A80 - 265
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 461 )A266 - 461
4X-RAY DIFFRACTION4chain 'A' and (resid 462 through 502 )A462 - 502
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 57 )B8 - 57
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 288 )B58 - 288
7X-RAY DIFFRACTION7chain 'B' and (resid 289 through 461 )B289 - 461
8X-RAY DIFFRACTION8chain 'B' and (resid 462 through 502 )B462 - 502
9X-RAY DIFFRACTION9chain 'C' and (resid 8 through 57 )C8 - 57
10X-RAY DIFFRACTION10chain 'C' and (resid 58 through 288 )C58 - 288
11X-RAY DIFFRACTION11chain 'C' and (resid 289 through 461 )C289 - 461
12X-RAY DIFFRACTION12chain 'C' and (resid 462 through 502 )C462 - 502

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