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- PDB-2yp9: Haemagglutinin of 2005 Human H3N2 Virus in Complex with Avian Rec... -

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Basic information

Entry
Database: PDB / ID: 2yp9
TitleHaemagglutinin of 2005 Human H3N2 Virus in Complex with Avian Receptor Analogue 3SLN
ComponentsHEMAGGLUTININ
KeywordsVIRAL PROTEIN / RECEPTOR BINDING / MEMBRANE FUSION / INFLUENZA VIRUS EVOLUTION / GLYCOPROTEIN
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
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
CARBON MONOXIDE / N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsXiong, X. / Lin, Y.P. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. / Liu, J. / Skehel, J.J. ...Xiong, X. / Lin, Y.P. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. / Liu, J. / Skehel, J.J. / Gamblin, S.J. / Hay, A.J. / Daniels, R.S. / McCauley, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Evolution of the Receptor Binding Properties of the Influenza A(H3N2) Hemagglutinin.
Authors: Lin, Y.P. / Xiong, X. / Wharton, S.A. / Martin, S.R. / Coombs, P.J. / Vachieri, S.G. / Christodoulou, E. / Walker, P.A. / Liu, J. / Skehel, J.J. / Gamblin, S.J. / Hay, A.J. / Daniels, R.S. / Mccauley, J.W.
History
DepositionOct 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references / Structure summary
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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_struct_special_symmetry / 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_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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

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Assembly

Deposited unit
A: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,82114
Polymers56,4881
Non-polymers3,33213
Water10,521584
1
A: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,46242
Polymers169,4653
Non-polymers9,99739
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area28160 Å2
ΔGint160.4 kcal/mol
Surface area60710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.970, 100.970, 387.190
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-4125-

HOH

21A-4219-

HOH

31A-4220-

HOH

41A-4224-

HOH

51A-4227-

HOH

61A-4235-

HOH

71A-4581-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEMAGGLUTININ / / HAEMAGGLUTININ


Mass: 56488.215 Da / Num. of mol.: 1 / Fragment: TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-519 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: H3N2Influenza A virus subtype H3N2 / Variant: A/HONG KONG/4443/2005 / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: I2D7A8

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Sugars , 4 types, 8 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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: isolated from a genetically manipulated source
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
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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
#7: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / 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

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Non-polymers , 4 types, 589 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE GLOBAL INITIATIVE ON SHARING ALL INFLUENZA DATA ( GISAID) ACCESSION NUMBER PROVIDED EPI347408

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.42 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP, DEGLYCOSYLATED PROTEIN, 0.1 M HEPES PH 7.5, 0.2 M KCL, 30% PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979493
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.79→46.96 Å / Num. obs: 71580 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→129.06 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.703 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19485 3620 5.1 %RANDOM
Rwork0.17166 ---
obs0.17285 67956 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.49 Å20 Å2
2--0.97 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.79→129.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 215 584 4672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024227
X-RAY DIFFRACTIONr_bond_other_d0.0010.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9955745
X-RAY DIFFRACTIONr_angle_other_deg0.9463.0036999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47624.975203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02815697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3961524
X-RAY DIFFRACTIONr_chiral_restr0.1060.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024601
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 245 -
Rwork0.306 4729 -
obs--99.68 %
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)
10.0681-0.03360.02950.0964-0.19830.87430.0056-0.0486-0.065-0.0170.05120.00780.0858-0.0437-0.05680.06710.003-0.03410.04860.02750.0951-45.61638.483659.3574
20.66590.2635-0.01310.60650.25230.7793-0.0232-0.21730.03910.12240.1186-0.05790.09070.1139-0.09540.08180.0396-0.04430.1856-0.01790.0386-39.416414.431192.7659
30.04670.03890.14760.12730.01270.92080.01580.0168-0.0381-0.03040.060.00810.03050.0611-0.07580.071-0.0116-0.03780.0661-0.00460.1073-49.718513.854538.1988
41.16770.1995-1.85012.8387-1.66713.77350.17180.00520.1123-0.1795-0.01520.0022-0.02070.0358-0.15660.15060.02360.03030.0352-0.03210.0526-45.893817.8379-4.7195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 127
2X-RAY DIFFRACTION2A128 - 263
3X-RAY DIFFRACTION3A264 - 448
4X-RAY DIFFRACTION4A449 - 503

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