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- PDB-5t08: Crystal structure of H6 hemagglutinin G225D mutant from Taiwan (2... -

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Basic information

Entry
Database: PDB / ID: 5t08
TitleCrystal structure of H6 hemagglutinin G225D mutant from Taiwan (2013) H6N1 influenza virus
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: 2.1895 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 16, 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)174,94810
Polymers174,0636
Non-polymers8854
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-141 kcal/mol
Surface area60460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.065, 98.364, 133.239
Angle α, β, γ (deg.)90.00, 126.48, 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: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.1895→50 Å / Num. obs: 96720 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 19.1
Reflection shellResolution: 2.1895→2.23 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: 4XKD

4xkd


Resolution: 2.1895→49.339 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2501 4798 4.96 %
Rwork0.2155 --
obs0.2172 96672 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1895→49.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 56 410 12376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212255
X-RAY DIFFRACTIONf_angle_d1.63516628
X-RAY DIFFRACTIONf_dihedral_angle_d19.6954537
X-RAY DIFFRACTIONf_chiral_restr0.0741791
X-RAY DIFFRACTIONf_plane_restr0.0112156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1895-2.21440.33781180.27062312X-RAY DIFFRACTION75
2.2144-2.24040.28341560.28133042X-RAY DIFFRACTION96
2.2404-2.26780.35381660.27272972X-RAY DIFFRACTION97
2.2678-2.29650.30381550.26193103X-RAY DIFFRACTION99
2.2965-2.32670.29611580.25263093X-RAY DIFFRACTION99
2.3267-2.35860.28131540.25443051X-RAY DIFFRACTION99
2.3586-2.39220.31151570.25043125X-RAY DIFFRACTION99
2.3922-2.4280.3011890.24673072X-RAY DIFFRACTION99
2.428-2.46590.28211550.24653057X-RAY DIFFRACTION98
2.4659-2.50630.29961590.2363079X-RAY DIFFRACTION98
2.5063-2.54950.26871530.23633011X-RAY DIFFRACTION97
2.5495-2.59590.26931710.23633040X-RAY DIFFRACTION98
2.5959-2.64580.26011620.23683112X-RAY DIFFRACTION99
2.6458-2.69980.30431520.2453124X-RAY DIFFRACTION99
2.6998-2.75850.29761610.24553139X-RAY DIFFRACTION99
2.7585-2.82270.29741560.24423094X-RAY DIFFRACTION99
2.8227-2.89330.32561640.23983097X-RAY DIFFRACTION99
2.8933-2.97150.29921670.2453059X-RAY DIFFRACTION99
2.9715-3.05890.27621650.22613071X-RAY DIFFRACTION98
3.0589-3.15760.24431460.22853022X-RAY DIFFRACTION96
3.1576-3.27050.27681500.22373136X-RAY DIFFRACTION99
3.2705-3.40140.24951730.22443097X-RAY DIFFRACTION99
3.4014-3.55610.21891630.21123070X-RAY DIFFRACTION99
3.5561-3.74360.23681740.18913136X-RAY DIFFRACTION99
3.7436-3.9780.23111460.18843093X-RAY DIFFRACTION98
3.978-4.2850.23411690.16763068X-RAY DIFFRACTION98
4.285-4.71590.1741610.15633158X-RAY DIFFRACTION100
4.7159-5.39760.19961600.17513145X-RAY DIFFRACTION100
5.3976-6.79760.21471560.22463118X-RAY DIFFRACTION98
6.7976-49.35120.25071820.24323178X-RAY DIFFRACTION98

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