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- PDB-2wre: structure of H2 japan hemagglutinin with human receptor -

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Basic information

Entry
Database: PDB / ID: 2wre
Titlestructure of H2 japan hemagglutinin with human receptor
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / 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 / 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 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.001 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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 / _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 16, 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
A: HEMAGGLUTININ
B: HEMAGGLUTININ
C: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,6406
Polymers171,2263
Non-polymers1,4143
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16200 Å2
ΔGint-44.51 kcal/mol
Surface area59160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.970, 117.460, 225.370
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
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 5:323 )
211CHAIN C AND (RESSEQ 8:323 )
112CHAIN B AND (RESSEQ 330:492 )
212CHAIN C AND (RESSEQ 330:492 )

NCS ensembles :
ID
1
2

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Components

#1: Protein HEMAGGLUTININ


Mass: 57075.293 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-505 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/JAPAN/305+/1957(H2N2))
References: UniProt: Q67085, UniProt: Q0A2X3*PLUS
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
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: 3.14 Å3/Da / Density % sol: 60.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 39715 / % possible obs: 98.6 % / Observed criterion σ(I): 2.6 / Redundancy: 6.6 % / Biso Wilson estimate: 68.5 Å2 / Rmerge(I) obs: 0.14

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Processing

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

Resolution: 3.001→19.98 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2946 1998 5 %
Rwork0.2387 --
obs0.2415 39715 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.673 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2776 Å20 Å20 Å2
2--1.6085 Å20 Å2
3---3.6691 Å2
Refinement stepCycle: LAST / Resolution: 3.001→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11347 0 96 0 11443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911735
X-RAY DIFFRACTIONf_angle_d1.21415862
X-RAY DIFFRACTIONf_dihedral_angle_d18.6754283
X-RAY DIFFRACTIONf_chiral_restr0.0761721
X-RAY DIFFRACTIONf_plane_restr0.0042043
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2475X-RAY DIFFRACTIONPOSITIONAL
12C2475X-RAY DIFFRACTIONPOSITIONAL0.048
21B1311X-RAY DIFFRACTIONPOSITIONAL
22C1311X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0014-3.07620.4106880.34661584X-RAY DIFFRACTION58
3.0762-3.15910.39631520.33342744X-RAY DIFFRACTION100
3.1591-3.25160.3431510.30922737X-RAY DIFFRACTION100
3.2516-3.35610.3931250.30642745X-RAY DIFFRACTION100
3.3561-3.47550.29121550.28752732X-RAY DIFFRACTION100
3.4755-3.61380.34661540.27472742X-RAY DIFFRACTION100
3.6138-3.77730.33591400.25122778X-RAY DIFFRACTION100
3.7773-3.97490.31251480.23972739X-RAY DIFFRACTION100
3.9749-4.22180.25391390.21282770X-RAY DIFFRACTION100
4.2218-4.54420.22691370.19522781X-RAY DIFFRACTION100
4.5442-4.9950.22291340.1912796X-RAY DIFFRACTION100
4.995-5.70310.27311670.1952773X-RAY DIFFRACTION100
5.7031-7.13060.28161490.21542857X-RAY DIFFRACTION100
7.1306-19.98020.29011590.21632939X-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)
10.531-0.3004-0.4060.63320.79854.126-0.10320.2723-0.0004-0.3701-0.0699-0.1644-0.19960.42350.14550.46380.00350.10170.44740.13350.343642.36985.8687-12.796
20.7024-0.0453-0.6971.29161.47662.7173-0.04140.1108-0.32240.2294-0.0269-0.07730.25040.04040.10290.43850.0518-0.0380.37380.09220.532141.2507-13.339-4.4549
30.41220.24880.43431.20921.05992.1564-0.05950.1122-0.029-0.1380.05470.2164-0.0908-0.053-0.02530.48910.0303-0.05940.47940.0940.457223.5393-2.197-9.4584
40.316-0.00850.20480.63421.10791.4373-0.0020.05660.1409-0.3844-0.0335-0.288-0.59550.16920.02910.6441-0.13410.06760.32710.13340.498448.46535.505528.6192
50.2416-0.08130.021.40631.69983.0020.0416-0.02350.08510.22120.0994-0.31480.47880.4283-0.10930.3641-0.0179-0.07840.35070.11020.465646.98315.436244.0635
60.2317-0.1657-0.33840.64130.82851.6595-0.0369-0.04590.0372-0.1919-0.24230.2193-0.3979-0.180.20980.37940.0569-0.05930.3924-0.030.315318.223522.429737.1366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 330:492
2X-RAY DIFFRACTION2CHAIN B AND RESID 330:492
3X-RAY DIFFRACTION3CHAIN C AND RESID 330:492
4X-RAY DIFFRACTION4CHAIN A AND RESID 8:323
5X-RAY DIFFRACTION5CHAIN B AND RESID 5:323
6X-RAY DIFFRACTION6CHAIN C AND RESID 8:323

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