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- PDB-5t0e: Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2... -

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Basic information

Entry
Database: PDB / ID: 5t0e
TitleCrystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza virus in complex with LSTa
Components
  • Hemagglutinin
  • Hemagglutinin HA2 chain
KeywordsIMMUNE SYSTEM / Influenza virus / hemagglutinin / HA / Taiwan (2013) H6N1 / Receptor specificity
Function / homology
Function and homology information


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
Similarity search - Function
Haemagglutinin, influenzavirus 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 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
Hemagglutinin HA2 chain / Hemagglutinin
Similarity search - Component
Biological speciesH6N1 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 Å
AuthorsWilson, I.A. / Tzarum, N. / Zhu, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI114730 United States
CitationJournal: EMBO Mol Med / Year: 2017
Title: A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human-type receptors.
Authors: de Vries, R.P. / Tzarum, N. / Peng, W. / Thompson, A.J. / Ambepitiya Wickramasinghe, I.N. / de la Pena, A.T.T. / van Breemen, M.J. / Bouwman, K.M. / Zhu, X. / McBride, R. / Yu, W. / Sanders, ...Authors: de Vries, R.P. / Tzarum, N. / Peng, W. / Thompson, A.J. / Ambepitiya Wickramasinghe, I.N. / de la Pena, A.T.T. / van Breemen, M.J. / Bouwman, K.M. / Zhu, X. / McBride, R. / Yu, W. / Sanders, R.W. / Verheije, M.H. / Wilson, I.A. / Paulson, J.C.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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.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_struct_assembly_gen.asym_id_list / _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
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin HA2 chain
C: Hemagglutinin
D: Hemagglutinin HA2 chain
E: Hemagglutinin
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,41911
Polymers174,0636
Non-polymers1,3565
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30490 Å2
ΔGint-142 kcal/mol
Surface area60910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.108, 99.206, 133.390
Angle α, β, γ (deg.)90.00, 126.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemagglutinin


Mass: 37389.191 Da / Num. of mol.: 3 / Mutation: G225D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) H6N1 subtype (virus) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X268
#2: Protein Hemagglutinin HA2 chain


Mass: 20631.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) H6N1 subtype (virus) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X267
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-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/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+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.: 4
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10mM NiCl2, 0.1M Tris pH 8.5, 20% (w/v) MPEG 2000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.0888→50 Å / Num. obs: 113368 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rsym value: 0.1 / Net I/σ(I): 18.3
Reflection shellResolution: 2.1→2.15 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T08

5t08


Resolution: 2.089→49.444 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 5700 5.03 %
Rwork0.2137 --
obs0.2156 113339 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.089→49.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 88 479 12477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212287
X-RAY DIFFRACTIONf_angle_d1.54216675
X-RAY DIFFRACTIONf_dihedral_angle_d18.5264545
X-RAY DIFFRACTIONf_chiral_restr0.1461801
X-RAY DIFFRACTIONf_plane_restr0.0122158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0888-2.11260.32371340.2682696X-RAY DIFFRACTION74
2.1126-2.13740.3222150.25823428X-RAY DIFFRACTION96
2.1374-2.16350.29832010.24773507X-RAY DIFFRACTION97
2.1635-2.19090.25671850.24293581X-RAY DIFFRACTION98
2.1909-2.21970.3121930.24013524X-RAY DIFFRACTION98
2.2197-2.25010.29111910.24743579X-RAY DIFFRACTION99
2.2501-2.28230.26911770.23853624X-RAY DIFFRACTION99
2.2823-2.31630.25411580.23233625X-RAY DIFFRACTION99
2.3163-2.35250.26551900.24313588X-RAY DIFFRACTION99
2.3525-2.39110.28381760.2333654X-RAY DIFFRACTION99
2.3911-2.43230.2852240.23553583X-RAY DIFFRACTION99
2.4323-2.47650.2852100.23453591X-RAY DIFFRACTION100
2.4765-2.52420.25712050.2283599X-RAY DIFFRACTION100
2.5242-2.57570.30291730.22783635X-RAY DIFFRACTION100
2.5757-2.63170.30391780.23413647X-RAY DIFFRACTION100
2.6317-2.69290.28921950.22833653X-RAY DIFFRACTION100
2.6929-2.76020.2461900.22783624X-RAY DIFFRACTION100
2.7602-2.83490.29731940.22713643X-RAY DIFFRACTION100
2.8349-2.91830.29441940.2363647X-RAY DIFFRACTION100
2.9183-3.01250.261930.2273587X-RAY DIFFRACTION100
3.0125-3.12010.25362070.21363630X-RAY DIFFRACTION100
3.1201-3.2450.27441860.21793631X-RAY DIFFRACTION100
3.245-3.39270.24131960.20393670X-RAY DIFFRACTION100
3.3927-3.57150.22381990.20213597X-RAY DIFFRACTION100
3.5715-3.79520.20361850.18283659X-RAY DIFFRACTION99
3.7952-4.08810.21671790.17763677X-RAY DIFFRACTION100
4.0881-4.49920.21711810.16843668X-RAY DIFFRACTION100
4.4992-5.14970.21880.16853676X-RAY DIFFRACTION100
5.1497-6.48580.25211940.22363677X-RAY DIFFRACTION100
6.4858-49.4580.27862090.26243739X-RAY DIFFRACTION99

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