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- PDB-5l14: The crystal structure of neuraminidase from A/Shanghai/2/2013 (H7... -

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Basic information

Entry
Database: PDB / ID: 5l14
TitleThe crystal structure of neuraminidase from A/Shanghai/2/2013 (H7N9) influenza virus
ComponentsNeuraminidase
KeywordsHYDROLASE / neuraminidase / H7N9
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
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, H. / Stevens, J.
CitationJournal: J. Infect. Dis. / Year: 2017
Title: Drug Susceptibility Evaluation of an Influenza A(H7N9) Virus by Analyzing Recombinant Neuraminidase Proteins.
Authors: Gubareva, L.V. / Sleeman, K. / Guo, Z. / Yang, H. / Hodges, E. / Davis, C.T. / Baranovich, T. / Stevens, J.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
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 / pdbx_struct_conn_angle / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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

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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)46,0764
Polymers44,2551
Non-polymers1,8213
Water7,566420
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,30316
Polymers177,0214
Non-polymers7,28312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area24850 Å2
ΔGint70 kcal/mol
Surface area46330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.865, 181.865, 181.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-938-

HOH

21A-1008-

HOH

31A-1020-

HOH

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Components

#1: Protein Neuraminidase /


Mass: 44255.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Shanghai/02/2013(H7N9))
Strain: A/Shanghai/02/2013(H7N9) / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NFR6, exo-alpha-sialidase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.1 M HEPES:NaOH pH 7.5, 25% PEG 1000

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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: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 40109 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 27.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WMJ

4wmj


Resolution: 1.9→35.667 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1834 2016 5.03 %
Rwork0.167 --
obs0.1679 40105 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→35.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 120 420 3595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043289
X-RAY DIFFRACTIONf_angle_d0.8784488
X-RAY DIFFRACTIONf_dihedral_angle_d11.9371221
X-RAY DIFFRACTIONf_chiral_restr0.035502
X-RAY DIFFRACTIONf_plane_restr0.004568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.26161580.24122636X-RAY DIFFRACTION98
1.9475-2.00020.23731350.24062662X-RAY DIFFRACTION98
2.0002-2.0590.24811330.20932667X-RAY DIFFRACTION99
2.059-2.12550.23611570.20432675X-RAY DIFFRACTION99
2.1255-2.20140.21161210.20552704X-RAY DIFFRACTION99
2.2014-2.28950.23841610.20082674X-RAY DIFFRACTION99
2.2895-2.39370.24171480.19542698X-RAY DIFFRACTION99
2.3937-2.51990.2471370.18832691X-RAY DIFFRACTION99
2.5199-2.67770.22021420.19012732X-RAY DIFFRACTION99
2.6777-2.88440.19421330.18222718X-RAY DIFFRACTION99
2.8844-3.17450.18421500.1682737X-RAY DIFFRACTION99
3.1745-3.63350.16691310.14912770X-RAY DIFFRACTION99
3.6335-4.57630.13441550.12552778X-RAY DIFFRACTION99
4.5763-35.67290.13811550.14382947X-RAY DIFFRACTION99
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)
10.3348-0.0895-0.07330.06370.04870.0613-0.0107-0.0169-0.05260.0140.0731-0.0005-0.0668-0.018800.2264-0.00860.00480.20120.00310.23487.3375-21.7244-49.5646
20.14960.00820.07860.1217-0.09530.11960.03250.0494-0.04510.00170.0014-0.0130.0752-0.0993-00.2178-0.0002-0.00110.1986-0.00990.247511.0465-12.0738-55.1195
30.03740.04440.02530.05140.03050.042-0.11640.24230.0028-0.11910.1014-0.1717-0.00460.1383-00.2593-0.00040.02150.2454-0.01610.270518.1767-6.6279-69.4291
40.01470.0342-0.03260.0776-0.04690.10520.0083-0.02150.11760.0222-0.03940.03240.00120.0371-00.19750.0011-0.00480.2102-0.01230.250512.785-8.3369-53.0256
50.06930.05380.07910.06890.04040.10290.0451-0.03530.1222-0.01640.0624-0.0989-0.02860.00780.00010.22410.00910.00980.2007-0.00260.273625.9694-5.1633-49.5225
60.0539-0.03760.0380.08890.01510.05760.0068-0.0470.0480.02870.0534-0.05370.09850.06440.00020.24140.0127-0.00010.1995-0.00630.265928.2211-15.4076-49.3392
70.4921-0.07450.40320.1889-0.09060.32750.0683-0.0303-0.06550.0543-0.0208-0.15150.02350.026900.23390.0114-0.01030.1956-0.00030.285229.8543-23.3512-47.46
80.2706-0.13310.11620.3754-0.07930.05060.0060.0401-0.0509-0.04250.0115-0.10550.08320.023400.23060.02460.00840.1984-0.01320.280619.83-34.8672-57.668
90.44420.01030.13580.35080.17650.1220.02950.05-0.0211-0.06680.00250.0320.0657-0.0462-00.20450.0163-0.00050.1818-0.01060.232711.6577-20.8551-58.4992
100.2195-0.02960.06580.21030.05910.0358-0.01790.1062-0.08320.00490.0088-0.024-0.0127-0.0295-0.00010.21710.00420.00250.2319-0.01030.27184.4573-24.5234-63.0146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 83 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 157 )
4X-RAY DIFFRACTION4chain 'A' and (resid 158 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 246 )
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 318 )
8X-RAY DIFFRACTION8chain 'A' and (resid 319 through 411 )
9X-RAY DIFFRACTION9chain 'A' and (resid 412 through 440 )
10X-RAY DIFFRACTION10chain 'A' and (resid 441 through 470 )

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