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- PDB-7nn9: NATIVE INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) -

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Basic information

Entry
Database: PDB / ID: 7nn9
TitleNATIVE INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN)
ComponentsNEURAMINIDASE N9
KeywordsHYDROLASE (O-GLYCOSYL) / NEURAMINIDASE / SIALIDASE
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 / Resolution: 2 Å
AuthorsVarghese, J.N. / Colman, P.M.
Citation
Journal: Protein Sci. / Year: 1995
Title: Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.
Authors: Varghese, J.N. / Epa, V.C. / Colman, P.M.
#1: Journal: Proteins / Year: 1992
Title: The Structure of the Complex between Influenza Virus Neuraminidase and Sialic Acid, the Viral Receptor
Authors: Varghese, J.N. / Mckimm-Breschkin, J.L. / Caldwell, J.B. / Kortt, A.A. / Colman, P.M.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
Authors: Tulip, W.R. / Varghese, J.N. / Baker, A.T. / Van Donkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
Authors: Varghese, J.N. / Colman, P.M.
#4: Journal: Proteins / Year: 1987
Title: The Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus
Authors: Baker, A.T. / Varghese, J.N. / Laver, W.G. / Air, G.M. / Colman, P.M.
#5: Journal: Virology / Year: 1985
Title: Gene and Protein Sequence of an Influenza Virus Neuraminidase with Hemagglutinin Activity
Authors: Air, G.M. / Ritchie, L.R. / Laver, W.G. / Colman, P.M.
#6: Journal: Virology / Year: 1984
Title: Influenza Virus Neuraminidase with Hemagglutinin Activity
Authors: Laver, W.G. / Colman, P.M. / Webster, R.G. / Hinshaw, V.S. / Air, G.M.
#7: Journal: Nature / Year: 1983
Title: Structure of the Influenza Virus Glycoprotein Antigen Neuraminidase at 2.9 Angstroms Resolution
Authors: Varghese, J.N. / Laver, W.G. / Colman, P.M.
History
DepositionMar 15, 1995Processing site: BNL
SupersessionApr 3, 1996ID: 2NN9
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.PDB_ins_code / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.PDB_ins_code_1 / _pdbx_validate_close_contact.PDB_ins_code_2 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEURAMINIDASE N9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4415
Polymers43,7241
Non-polymers1,7184
Water3,981221
1
A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,76520
Polymers174,8954
Non-polymers6,87016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)182.800, 182.800, 182.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Atom site foot note1: CIS PROLINE - PRO 326 / 2: CIS PROLINE - PRO 431

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Components

#1: Protein NEURAMINIDASE N9 / SIALIDASE


Mass: 43723.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, 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-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Source detailsMOLECULE_NAME: N9 NEURAMINIDASE. GROWN IN CHICK EMBRYO (HEN EGG).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
21.7 Mpotassium phosphate1drop
31.9 Mpotassium phosphate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 33570 / % possible obs: 66 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.012
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.012
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.2 Å / Rmerge(I) obs: 0.175

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Processing

Software
NameClassification
R-AXISdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 2→6 Å / σ(F): 2
Details: ATOMS WITH ZERO OCCUPANCY WERE DUMMY ATOMS AT THE REFINEMENT STAGE.
RfactorNum. reflection
Rwork0.152 -
obs0.152 28477
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 112 221 3400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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