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Basic information

Entry
Database: PDB / ID: 4wea
TitleStructure and receptor binding prefereneces of recombinant human A(H3N2) virus hemagglutinins
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Hemagglutinin / H3N2 / influenza virus
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
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
CitationJournal: Virology / Year: 2015
Title: Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Guo, Z. / Villanueva, J.M. / Stevens, J.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2017Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_keywords / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr2_label_asym_id / _struct_keywords.text / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / refine_hist / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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 3.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,12310
Polymers57,8411
Non-polymers2,2829
Water2,882160
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,36930
Polymers173,5223
Non-polymers6,84627
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area22660 Å2
ΔGint55 kcal/mol
Surface area59860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.733, 100.733, 382.613
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hemagglutinin


Mass: 57840.719 Da / Num. of mol.: 1 / Fragment: unp residues 17-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Singapore/H2011.447/2011(H3N2) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R9U684
#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.: 1 / Source method: obtained synthetically
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: 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.: 7 / Source method: obtained synthetically / 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
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 10.5 / Details: 0.1M CAPS:NaOH, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38431 / % possible obs: 99.6 % / Redundancy: 6.9 % / Net I/σ(I): 7.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.2→35.039 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1922 5 %
Rwork0.1895 --
obs0.1912 38413 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 146 160 4187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064122
X-RAY DIFFRACTIONf_angle_d1.0215580
X-RAY DIFFRACTIONf_dihedral_angle_d15.9371517
X-RAY DIFFRACTIONf_chiral_restr0.073623
X-RAY DIFFRACTIONf_plane_restr0.004719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.30811400.23032478X-RAY DIFFRACTION96
2.255-2.3160.25151360.21482545X-RAY DIFFRACTION99
2.316-2.38410.24881140.20692630X-RAY DIFFRACTION100
2.3841-2.46110.21821300.19912574X-RAY DIFFRACTION100
2.4611-2.5490.26141510.20762570X-RAY DIFFRACTION100
2.549-2.6510.25741290.19882613X-RAY DIFFRACTION100
2.651-2.77160.25191440.20252566X-RAY DIFFRACTION100
2.7716-2.91770.23221410.20122594X-RAY DIFFRACTION100
2.9177-3.10040.2451530.20122581X-RAY DIFFRACTION100
3.1004-3.33960.22181190.20132630X-RAY DIFFRACTION100
3.3396-3.67530.20381490.18752613X-RAY DIFFRACTION100
3.6753-4.20640.21291440.1682638X-RAY DIFFRACTION100
4.2064-5.29670.18271320.15782676X-RAY DIFFRACTION100
5.2967-35.04380.22641400.20132783X-RAY DIFFRACTION99
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)
10.70740.1497-0.35970.46340.19860.54640.1204-0.1512-0.09010.0690.13760.06530.5445-0.4010.00480.3796-0.0265-0.11280.1757-0.00710.4174-2.658738.5248-32.9904
20.3328-0.5354-0.20330.42970.20020.6282-0.0373-0.7355-0.33990.56930.1443-0.1760.47370.50790.00150.97050.0394-0.25430.95820.23760.51899.947635.10217.8263
30.0595-0.2226-0.02670.91350.0970.0854-0.0592-0.93510.02190.28270.2518-0.32280.00180.02980.27561.05120.0673-0.29821.45770.09440.481317.210545.385229.1233
40.2510.05490.06870.05230.04440.0271-0.5267-0.37680.40440.95240.3-0.0288-0.2143-0.3694-0.00061.41410.0758-0.03331.4627-0.02320.55657.37248.441333.8132
50.6928-0.35540.02370.3229-0.04010.1364-0.1814-1.10020.40730.62580.24180.11170.54670.2175-0.0051.1568-0.0277-0.14771.19160.07080.53896.036145.379125.9922
60.507-0.2734-0.48260.28410.04481.34410.0494-0.4206-0.11690.39150.2203-0.0690.16670.48720.31560.70780.014-0.20740.68120.11370.435211.563839.76211.8669
70.4115-0.1965-0.12780.38490.38090.92510.0543-0.0927-0.18380.02580.0732-0.03390.5159-0.17940.00020.3812-0.0243-0.07580.21890.01720.4126-0.766739.3676-33.7484
80.2455-0.23260.55530.68570.23771.04690.1301-0.2091-0.17240.31480.1312-0.1170.32180.61760.31390.4994-0.0233-0.08820.36190.01860.45125.086944.9001-19.3165
9-0.01140.02090.26940.38850.3490.25620.0865-0.0422-0.11440.01180.05580.0088-0.0822-0.0529-00.2668-0.0064-0.01770.26020.00210.3714-1.329251.7416-28.8422
100.0325-0.18170.09990.4763-0.05790.34530.0690.26280.0337-0.3521-0.06720.01210.0083-0.1025-0.00140.43140.03750.00560.3879-0.08280.41683.800245.9583-70.2222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 184 )
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 214 through 247 )
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 275 )
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 366 )
8X-RAY DIFFRACTION8chain 'A' and (resid 367 through 404 )
9X-RAY DIFFRACTION9chain 'A' and (resid 405 through 455 )
10X-RAY DIFFRACTION10chain 'A' and (resid 456 through 502 )

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