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- PDB-6n5a: Crystal structure of an equine H7 hemagglutinin from A/equine/NY/... -

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Basic information

Entry
Database: PDB / ID: 6n5a
TitleCrystal structure of an equine H7 hemagglutinin from A/equine/NY/49/73 (H7N7)
Components(HEMAGGLUTININ ...) x 2
KeywordsVIRAL PROTEIN / equine / H7 / hemagglutinin / N-glycolylneuraminic acid / receptor specificity
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 / virion membrane
Similarity search - Function
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 ...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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R%6 AI117675 United States
CitationJournal: Cell Rep / Year: 2019
Title: N-Glycolylneuraminic Acid as a Receptor for Influenza A Viruses.
Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / ...Authors: Broszeit, F. / Tzarum, N. / Zhu, X. / Nemanichvili, N. / Eggink, D. / Leenders, T. / Li, Z. / Liu, L. / Wolfert, M.A. / Papanikolaou, A. / Martinez-Romero, C. / Gagarinov, I.A. / Yu, W. / Garcia-Sastre, A. / Wennekes, T. / Okamatsu, M. / Verheije, M.H. / Wilson, I.A. / Boons, G.J. / de Vries, R.P.
History
DepositionNov 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 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 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMAGGLUTININ HA1 SUBUNIT
B: HEMAGGLUTININ HA2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,10312
Polymers58,8322
Non-polymers1,27110
Water39622
1
A: HEMAGGLUTININ HA1 SUBUNIT
B: HEMAGGLUTININ HA2 SUBUNIT
hetero molecules

A: HEMAGGLUTININ HA1 SUBUNIT
B: HEMAGGLUTININ HA2 SUBUNIT
hetero molecules

A: HEMAGGLUTININ HA1 SUBUNIT
B: HEMAGGLUTININ HA2 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,31036
Polymers176,4966
Non-polymers3,81430
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area39460 Å2
ΔGint-105 kcal/mol
Surface area55450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.404, 87.404, 524.848
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-408-

SO4

21A-409-

SO4

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Components

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HEMAGGLUTININ ... , 2 types, 2 molecules AB

#1: Protein HEMAGGLUTININ HA1 SUBUNIT


Mass: 37298.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/equine/New York/49/1973(H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A348FV55
#2: Protein HEMAGGLUTININ HA2 SUBUNIT


Mass: 21533.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/equine/New York/49/1973(H7N7) / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A348FV55

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Sugars , 1 types, 2 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 30 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 4.92 Å3/Da / Density % sol: 74.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 6.5, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 19888 / % possible obs: 99.8 % / Redundancy: 15.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.05 / Net I/σ(I): 8.4
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1 / Num. unique obs: 961 / CC1/2: 0.73 / Rpim(I) all: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BSG

4bsg


Resolution: 3.3→46.24 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.869 / SU B: 16.434 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.87 / ESU R Free: 0.372 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23738 986 5.1 %RANDOM
Rwork0.19997 ---
obs0.20181 18177 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.1 Å2-0 Å2
2---0.21 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: 1 / Resolution: 3.3→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 80 22 3940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134004
X-RAY DIFFRACTIONr_bond_other_d0.0030.0183603
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.6625387
X-RAY DIFFRACTIONr_angle_other_deg1.4241.5938406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2225481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4523.2225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.18515694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8661525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024453
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02827
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_it8.6428.4741936
X-RAY DIFFRACTIONr_mcbond_other8.6428.4721935
X-RAY DIFFRACTIONr_mcangle_it13.40312.7052413
X-RAY DIFFRACTIONr_mcangle_other13.40112.7082414
X-RAY DIFFRACTIONr_scbond_it7.8618.9112068
X-RAY DIFFRACTIONr_scbond_other7.8698.9242061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.36213.1732962
X-RAY DIFFRACTIONr_long_range_B_refined18.946155.68716168
X-RAY DIFFRACTIONr_long_range_B_other18.945155.68916168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 77 -
Rwork0.276 1297 -
obs--99.93 %

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