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- PDB-3nn9: REFINED ATOMIC STRUCTURES OF N9 SUBTYPE INFLUENZA VIRUS NEURAMINI... -

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Basic information

Entry
Database: PDB / ID: 3nn9
TitleREFINED ATOMIC STRUCTURES OF N9 SUBTYPE INFLUENZA VIRUS NEURAMINIDASE AND ESCAPE MUTANTS
ComponentsNEURAMINIDASE N9
KeywordsHYDROLASE(O-GLYCOSYL)
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 speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsTulip, W.R. / Varghese, J.N. / Baker, A.T. / Vandonkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
Citation
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.
#1: 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.
#2: Journal: Proteins / Year: 1987
Title: 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.
#3: 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.
#4: Journal: Virology / Year: 1984
Title: Influenza Virus Neuraminidase with Hemmagglutinin Activity
Authors: Laver, W.G. / Colman, P.M. / Webster, R.G. / Hinshaw, V.S. / Air, G.M.
History
DepositionMar 28, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: 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: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _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_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 / _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_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAMINIDASE N9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4425
Polymers43,7251
Non-polymers1,7184
Water1,60389
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)181,76920
Polymers174,8994
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)185.100, 185.100, 185.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Atom site foot note1: RESIDUES 326 AND 431 ARE CIS PROLINES.

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Components

#1: Protein NEURAMINIDASE N9


Mass: 43724.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / 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)]beta-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]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/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 / 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1drop
210 mg/mlprotein1drop
31.9 Mpotassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. obs: 17915 / % possible obs: 68.6 % / Num. measured all: 104979 / Rmerge(I) obs: 0.121

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.3→6 Å / Rfactor Rwork: 0.178
Details: SIDE CHAINS AND/OR WHOLE RESIDUES WERE OMITTED FROM THE CRYSTALLOGRAPHIC REFINEMENT BY ASSIGNING THEM OCCUPANCIES OF 0.02. BECAUSE AN ERROR IN THE REGISTRATION OF THE NEURAMINIDASE C- ...Details: SIDE CHAINS AND/OR WHOLE RESIDUES WERE OMITTED FROM THE CRYSTALLOGRAPHIC REFINEMENT BY ASSIGNING THEM OCCUPANCIES OF 0.02. BECAUSE AN ERROR IN THE REGISTRATION OF THE NEURAMINIDASE C-TERMINAL SEGMENT WAS DISCOVERED LATE IN THE REFINEMENT PROCESS, THE COORDINATES OF RESIDUES 458 - 468 IN THIS MUTANT WERE TAKEN DIRECTLY FROM THE REFINED COORDINATES OF S370L. THE OCCUPANCY AND B VALUE OF THE CALCIUM ION ARE TENTATIVE AND REQUIRE HIGH RESOLUTION DATA REFINEMENT. THE CALCIUM WAS REFINED AS A NON-BONDED ION. THE FIVE LIGANDS ARE O ASP 293, O GLY 297, OD2 ASP 324, O ASN 347, AND HOH 8. THEY ARE IN OCTAHEDRAL GEOMETRY (NO RESTRAINTS WERE IMPOSED) AND THE SIXTH LIGAND (PRESUMABLY ANOTHER WATER MOLECULE) IS NOT SEEN IN THE ELECTRON DENSITY MAPS.
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 112 89 3268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
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
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 4

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