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- PDB-4wa3: The crystal structure of neuraminidase from a H3N8 influenza viru... -

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Basic information

Entry
Database: PDB / ID: 4wa3
TitleThe crystal structure of neuraminidase from a H3N8 influenza virus isolated from New England harbor seals
ComponentsNeuraminidase
KeywordsVIRAL PROTEIN / neuraminidase / influenza virus / seal
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / NICKEL (II) ION / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsYang, H. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J.
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Functional Analysis of Surface Proteins from an A(H3N8) Influenza Virus Isolated from New England Harbor Seals.
Authors: Yang, H. / Nguyen, H.T. / Carney, P.J. / Guo, Z. / Chang, J.C. / Jones, J. / Davis, C.T. / Villanueva, J.M. / Gubareva, L.V. / Stevens, J.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / refine_hist / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 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: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4205
Polymers42,9361
Non-polymers4844
Water6,053336
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,68220
Polymers171,7454
Non-polymers1,93716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation3_565-y,x+1,z1
crystal symmetry operation4_455y-1,-x,z1
Buried area16450 Å2
ΔGint-120 kcal/mol
Surface area45360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.816, 90.816, 110.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 42936.332 Da / Num. of mol.: 1 / Fragment: UNP residues 81-468
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/harbor seal/Massachusetts/1/2011(H3N8))
Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I6NW33

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Sugars , 2 types, 2 molecules

#2: 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.: 1
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
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 338 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.01 M nickel chloride, 0.1 M Tris-HCl, pH 8.5, 20% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2013
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 60962 / Num. obs: 39209 / % possible obs: 94.9 % / Redundancy: 2.7 % / Net I/σ(I): 20.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HT5

2ht5


Resolution: 1.801→29.195 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1741 1982 5.06 %
Rwork0.1629 --
obs0.1635 39185 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→29.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3009 0 26 336 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063117
X-RAY DIFFRACTIONf_angle_d1.1244215
X-RAY DIFFRACTIONf_dihedral_angle_d14.5331126
X-RAY DIFFRACTIONf_chiral_restr0.068454
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.84620.20461480.18082303X-RAY DIFFRACTION83
1.8462-1.89620.21381520.18062457X-RAY DIFFRACTION89
1.8962-1.95190.19281500.16242498X-RAY DIFFRACTION90
1.9519-2.01490.19361310.16872617X-RAY DIFFRACTION93
2.0149-2.08690.18031630.16312569X-RAY DIFFRACTION94
2.0869-2.17050.19141180.16142693X-RAY DIFFRACTION94
2.1705-2.26920.1981270.15962625X-RAY DIFFRACTION94
2.2692-2.38880.15331360.14822675X-RAY DIFFRACTION95
2.3888-2.53840.16291210.15472777X-RAY DIFFRACTION99
2.5384-2.73420.16091250.16352832X-RAY DIFFRACTION100
2.7342-3.00910.19551510.17582788X-RAY DIFFRACTION100
3.0091-3.4440.18791700.16762751X-RAY DIFFRACTION99
3.444-4.33680.1441600.14682805X-RAY DIFFRACTION99
4.3368-29.19910.17231300.17212813X-RAY DIFFRACTION98
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)
10.1011-0.026-0.02930.0725-0.03330.0229-0.00390.035-0.0652-0.0187-0.0084-0.0226-0.00310.05630.00010.1645-0.0004-0.00430.1661-0.00690.1376-53.403528.3173121.2008
20.00360.00160.0024-0.0015-0.00680.00660.0043-0.0709-0.05730.0723-0.00890.04440.023-0.0905-00.2393-0.01480.02880.20320.0120.1596-63.794938.5201138.4462
30.36280.05280.00040.43430.04670.2248-0.00410.0072-0.08150.00160.01140.060.0071-0.009300.1243-0.00090.00590.13050.00040.1455-63.86821.5407122.1125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 133 )
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 154 )
3X-RAY DIFFRACTION3chain 'A' and (resid 155 through 468 )

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