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- PDB-4we8: The crystal structure of hemagglutinin of influenza virus A/Victo... -

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Basic information

Entry
Database: PDB / ID: 4we8
TitleThe crystal structure of hemagglutinin of influenza virus A/Victoria/361/2011
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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_gen / 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_gen.asym_id_list / _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 / 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 / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8149
Polymers57,8411
Non-polymers1,9738
Water4,918273
1
A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules

A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,44127
Polymers173,5223
Non-polymers5,91924
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area20740 Å2
ΔGint59 kcal/mol
Surface area60710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.911, 100.911, 383.361
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
11A-778-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.25 Å3/Da / Density % sol: 62.12 %
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: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 43789 / Num. obs: 43789 / % possible obs: 98.5 % / Redundancy: 5.1 % / Net I/σ(I): 37.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementResolution: 2.1→34.156 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2218 5.07 %
Rwork0.1904 --
obs0.1923 43789 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 126 273 4280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054102
X-RAY DIFFRACTIONf_angle_d0.9315552
X-RAY DIFFRACTIONf_dihedral_angle_d16.1771542
X-RAY DIFFRACTIONf_chiral_restr0.063617
X-RAY DIFFRACTIONf_plane_restr0.003717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0997-2.14530.2981350.23472459X-RAY DIFFRACTION95
2.1453-2.19520.2661410.22732541X-RAY DIFFRACTION97
2.1952-2.25010.21831410.21432506X-RAY DIFFRACTION98
2.2501-2.31090.25691440.20672554X-RAY DIFFRACTION98
2.3109-2.37890.27891440.21232560X-RAY DIFFRACTION99
2.3789-2.45570.25071330.2082600X-RAY DIFFRACTION99
2.4557-2.54340.24881400.20762606X-RAY DIFFRACTION99
2.5434-2.64520.2291180.20062612X-RAY DIFFRACTION99
2.6452-2.76560.25751420.20852588X-RAY DIFFRACTION99
2.7656-2.91130.24911400.20312611X-RAY DIFFRACTION99
2.9113-3.09360.2371320.1992624X-RAY DIFFRACTION99
3.0936-3.33230.21131400.1972640X-RAY DIFFRACTION99
3.3323-3.66720.22631280.18432646X-RAY DIFFRACTION100
3.6672-4.19710.18941490.17072639X-RAY DIFFRACTION99
4.1971-5.28470.20311410.15842679X-RAY DIFFRACTION99
5.2847-34.16070.2361500.19572706X-RAY DIFFRACTION96

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