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- PDB-2wr7: the structure of influenza H2 human singapore hemagglutinin with ... -

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Basic information

Entry
Database: PDB / ID: 2wr7
Titlethe structure of influenza H2 human singapore hemagglutinin with human receptor
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN / LIPROPROTEIN
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 ...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 / 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: 2.5 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
DepositionAug 30, 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.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 / _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

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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)172,3294
Polymers171,4933
Non-polymers8371
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15090 Å2
ΔGint-42.33 kcal/mol
Surface area58540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.168, 123.678, 222.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEMAGGLUTININ /


Mass: 57164.238 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-506 / Source method: isolated from a natural source
Source: (natural) INFLUENZA A VIRUS (A/SINGAPORE/1/1957(H2N2))
References: UniProt: B4UR26, UniProt: Q67333*PLUS
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.2 % / 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: 2.5→30 Å / Num. obs: 74378 / % possible obs: 99.4 % / Observed criterion σ(I): 3.5 / Redundancy: 6.8 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.11

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Processing

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

Resolution: 2.5→8 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 32.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 3742 5 %
Rwork0.2388 --
obs0.2417 74377 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.143 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.612 Å20 Å20 Å2
2--2.407 Å20 Å2
3---0.205 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11251 0 57 348 11656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111596
X-RAY DIFFRACTIONf_angle_d1.32615674
X-RAY DIFFRACTIONf_dihedral_angle_d18.8574223
X-RAY DIFFRACTIONf_chiral_restr0.0841694
X-RAY DIFFRACTIONf_plane_restr0.0062030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53070.50431260.43442372X-RAY DIFFRACTION93
2.5307-2.56290.41631290.38942597X-RAY DIFFRACTION100
2.5629-2.59680.37471470.36332601X-RAY DIFFRACTION100
2.5968-2.63260.39741170.33792634X-RAY DIFFRACTION100
2.6326-2.67050.38621220.34022609X-RAY DIFFRACTION100
2.6705-2.71060.40561490.32282574X-RAY DIFFRACTION100
2.7106-2.75330.37031470.30212605X-RAY DIFFRACTION100
2.7533-2.79870.3871390.29812581X-RAY DIFFRACTION100
2.7987-2.84740.36621270.28662623X-RAY DIFFRACTION100
2.8474-2.89960.35571200.28162617X-RAY DIFFRACTION100
2.8996-2.95590.32491440.27812629X-RAY DIFFRACTION100
2.9559-3.01680.34931380.27472585X-RAY DIFFRACTION100
3.0168-3.0830.33371570.27372611X-RAY DIFFRACTION100
3.083-3.15550.31981460.26122581X-RAY DIFFRACTION100
3.1555-3.23530.2981330.25572629X-RAY DIFFRACTION100
3.2353-3.32390.34141440.25932624X-RAY DIFFRACTION100
3.3239-3.4230.34211360.24862643X-RAY DIFFRACTION100
3.423-3.53510.31031300.23692616X-RAY DIFFRACTION100
3.5351-3.66350.2581670.21792611X-RAY DIFFRACTION100
3.6635-3.81290.27461400.20462630X-RAY DIFFRACTION100
3.8129-3.99010.25031290.20462653X-RAY DIFFRACTION100
3.9901-4.20560.26031310.18742649X-RAY DIFFRACTION100
4.2056-4.47680.25491360.1842646X-RAY DIFFRACTION100
4.4768-4.8350.1951610.16842617X-RAY DIFFRACTION100
4.835-5.34490.22921440.1772684X-RAY DIFFRACTION100
5.3449-6.1730.241460.19292698X-RAY DIFFRACTION100
6.173-7.99990.28731370.22122716X-RAY DIFFRACTION100
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)
10.08560.1362-0.32170.3168-0.68181.76670.0779-0.2315-0.01930.0424-0.10670.07-0.03840.07390.01790.1553-0.0328-0.00220.45690.09630.1595-4.20142.85614.4299
20.3067-0.58570.94750.7295-1.41383.51750.0920.05660.04650.0265-0.0837-0.0030.11640.2008-0.02410.3038-0.0272-0.05170.280.04850.307916.0413-2.14410.1559
30.3581-0.03470.45290.7173-1.20482.86770.1921-0.0211-0.1808-0.1098-0.0068-0.09950.4954-0.1422-0.16450.4955-0.0998-0.15290.24040.09230.3440.8034-14.7043.3258
40.5747-0.33590.6680.0771-0.07160.9923-0.0284-0.17590.02170.00320.08660.1058-0.2729-0.3337-0.02490.34080.1472-0.01180.31320.00120.3519-16.241630.4297-27.5227
5-0.11730.2174-0.19140.3911-0.57261.4650.002-0.058-0.02580.0002-0.0722-0.0542-0.15130.17760.08140.28070.0182-0.00880.32940.02060.292416.216822.5042-35.4898
60.1150.20830.51680.5362-0.20242.0402-0.0327-0.02630.04870.01650.00430.02610.2453-0.2139-0.00370.2901-0.0184-0.03860.27290.00610.273-9.32810.7719-42.9718
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 330:487
2X-RAY DIFFRACTION2CHAIN B AND RESID 330:492
3X-RAY DIFFRACTION3CHAIN C AND RESID 330:478
4X-RAY DIFFRACTION4CHAIN A AND RESID 9:323
5X-RAY DIFFRACTION5CHAIN B AND RESID 5:323
6X-RAY DIFFRACTION6CHAIN C AND RESID 7:323

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