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- PDB-2yp8: Haemagglutinin of 2005 Human H3N2 Virus in Complex with Human Rec... -

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Basic information

Entry
Database: PDB / ID: 2yp8
TitleHaemagglutinin of 2005 Human H3N2 Virus in Complex with Human Receptor Analogue 6SLN
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
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,01414
Polymers56,4881
Non-polymers3,52613
Water9,188510
1
A: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
hetero molecules

A: HEMAGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,04142
Polymers169,4653
Non-polymers10,57739
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 area28400 Å2
ΔGint162.5 kcal/mol
Surface area61610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.920, 100.920, 386.690
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-2194-

HOH

21A-2198-

HOH

31A-2201-

HOH

41A-2206-

HOH

51A-2510-

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: 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, 9 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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


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 , 3 types, 514 molecules

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


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.33 % / 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: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→46.99 Å / Num. obs: 70771 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→128.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.687 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19818 3575 5.1 %RANDOM
Rwork0.17286 ---
obs0.17412 67196 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.8→128.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3873 0 228 510 4611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024246
X-RAY DIFFRACTIONr_bond_other_d0.0010.022893
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9985772
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0037020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08524.95202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82115697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2361524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02815
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 256 -
Rwork0.292 4629 -
obs--100 %
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)
10.0732-0.0301-0.01410.1194-0.12790.773-0.0034-0.0495-0.06740.00550.05210.00620.0721-0.0064-0.04870.07320.0051-0.03340.05340.03610.0886-44.25137.268167.2875
20.52020.08580.20940.35980.290.3027-0.0111-0.1458-0.00680.12930.0952-0.09890.06010.0395-0.08410.09470.015-0.03830.1481-0.00770.0414-39.353217.087291.8617
30.05590.03920.12930.1239-0.01960.66280.02250.0233-0.0466-0.02110.06230.00120.01870.0539-0.08480.0768-0.0104-0.0390.0698-0.01080.0894-49.714413.891738.2731
40.93440.2023-0.92221.4766-1.63022.37810.16160.03020.1126-0.1018-0.00670.03790.00360.0277-0.15490.11640.01080.02220.0606-0.04080.0475-46.178617.9148-4.8689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 157
2X-RAY DIFFRACTION2A158 - 263
3X-RAY DIFFRACTION3A264 - 448
4X-RAY DIFFRACTION4A449 - 503

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