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- PDB-2wrg: structure of H1 1918 hemagglutinin with human receptor -

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Basic information

Entry
Database: PDB / ID: 2wrg
Titlestructure of H1 1918 hemagglutinin with human receptor
Components
  • HEMAGGLUTININ HA1 CHAIN
  • HEMAGGLUTININ HA2 CHAIN
KeywordsVIRAL PROTEIN / ENVELOPE PROTEIN / GLYCOPROTEIN / LIPOPROTEIN
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; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / OTHER / Resolution: 3 Å
AuthorsLiu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: From the Cover: Structures of Receptor Complexes Formed by Hemagglutinins from the Asian Influenza Pandemic of 1957.
Authors: Liu, J. / Stevens, D.J. / Haire, L.F. / Walker, P.A. / Coombs, P.J. / Russell, R.J. / Gamblin, S.J. / Skehel, J.J.
History
DepositionSep 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_chiral / 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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
H: HEMAGGLUTININ HA1 CHAIN
I: HEMAGGLUTININ HA2 CHAIN
J: HEMAGGLUTININ HA1 CHAIN
K: HEMAGGLUTININ HA2 CHAIN
L: HEMAGGLUTININ HA1 CHAIN
M: HEMAGGLUTININ HA2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,40918
Polymers183,1396
Non-polymers3,27012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-2.76 kcal/mol
Surface area57760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.758, 156.843, 157.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN H AND (RESSEQ 7:42 OR RESSEQ 44:49 OR RESSEQ 49:132 OR RESSEQ 132:323 )
211CHAIN J AND (RESSEQ 7:42 OR RESSEQ 44:49 OR RESSEQ 49:132 OR RESSEQ 132:323 )
311CHAIN L AND (RESSEQ 7:42 OR RESSEQ 44:49 OR RESSEQ 49:132 OR RESSEQ 132:323 )
112CHAIN I AND (RESSEQ 501:660 )
212CHAIN K AND (RESSEQ 501:660 )
312CHAIN M AND (RESSEQ 501:660 )

NCS ensembles :
ID
1
2

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Components

#1: Protein HEMAGGLUTININ HA1 CHAIN


Mass: 35999.309 Da / Num. of mol.: 3 / Fragment: RESIDUES 18-343 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/BREVIG MISSION/1/1918(H1N1))
References: UniProt: Q9WFX3
#2: Protein HEMAGGLUTININ HA2 CHAIN


Mass: 25047.072 Da / Num. of mol.: 3 / Fragment: RESIDUES 345-566 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/BREVIG MISSION/1/1918(H1N1))
References: UniProt: Q9WFX3
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a3-b1_b4-c1_c6-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}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.: 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
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: 3.54 Å3/Da / Density % sol: 68.9 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 46270 / % possible obs: 98.5 % / Observed criterion σ(I): 1.3 / Redundancy: 5.1 % / Biso Wilson estimate: 77.87 Å2 / Rmerge(I) obs: 0.16

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3→29.68 Å / SU ML: 2.41 / σ(F): 0.02 / Phase error: 30.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3078 2366 5.1 %
Rwork0.2683 --
obs0.2703 46270 87.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.06 Å2 / ksol: 0.282 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.0484 Å20 Å2-0 Å2
2---1.6006 Å2-0 Å2
3----18.4478 Å2
Refinement stepCycle: LAST / Resolution: 3→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11397 0 222 0 11619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911908
X-RAY DIFFRACTIONf_angle_d1.20416160
X-RAY DIFFRACTIONf_dihedral_angle_d20.254267
X-RAY DIFFRACTIONf_chiral_restr0.0781782
X-RAY DIFFRACTIONf_plane_restr0.0042082
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11H2470X-RAY DIFFRACTIONPOSITIONAL
12J2470X-RAY DIFFRACTIONPOSITIONAL0.05
13L2470X-RAY DIFFRACTIONPOSITIONAL0.049
21I1282X-RAY DIFFRACTIONPOSITIONAL
22K1282X-RAY DIFFRACTIONPOSITIONAL0.068
23M1282X-RAY DIFFRACTIONPOSITIONAL0.067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06120.44931140.39222182X-RAY DIFFRACTION75
3.0612-3.12770.38541250.36762234X-RAY DIFFRACTION77
3.1277-3.20040.44441140.35542356X-RAY DIFFRACTION80
3.2004-3.28030.36191290.34622363X-RAY DIFFRACTION81
3.2803-3.36890.36061390.31482401X-RAY DIFFRACTION83
3.3689-3.46790.31671290.30132446X-RAY DIFFRACTION85
3.4679-3.57960.27821250.29072460X-RAY DIFFRACTION84
3.5796-3.70740.35151220.26662545X-RAY DIFFRACTION87
3.7074-3.85550.30911450.2592577X-RAY DIFFRACTION88
3.8555-4.03060.26911360.24342592X-RAY DIFFRACTION88
4.0306-4.24250.32111420.23072600X-RAY DIFFRACTION89
4.2425-4.50740.25371710.22052719X-RAY DIFFRACTION93
4.5074-4.85410.21481540.20252758X-RAY DIFFRACTION94
4.8541-5.340.25511420.21232812X-RAY DIFFRACTION95
5.34-6.10690.2611570.22212897X-RAY DIFFRACTION97
6.1069-7.6720.26541620.23722950X-RAY DIFFRACTION98
7.672-29.68120.25421600.23673012X-RAY DIFFRACTION96

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