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- PDB-1ncd: REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE... -

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Entry
Database: PDB / ID: 1ncd
TitleREFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX
Components
  • (IGG2A-KAPPA NC41 FAB ...) x 2
  • INFLUENZA A SUBTYPE N9 NEURAMINIDASE
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / exo-alpha-sialidase / exo-alpha-sialidase activity / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / viral budding from plasma membrane / response to bacterium / positive regulation of immune response / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane / plasma membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin heavy constant gamma 2A / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsTulip, W.R. / Varghese, J.N. / Colman, P.M.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex.
Authors: Tulip, W.R. / Varghese, J.N. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal Structures of Two Mutant Neuraminidase-Antibody Complexes with Amino Acid Substitutions in the Interface
Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Laver, W.G. / Colman, P.M.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1989
Title: Crystal Structures of Neuraminidase-Antibody Complexes
Authors: Tulip, W.R. / Varghese, J.N. / Webster, R.G. / Air, G.M. / Laver, W.G. / Colman, P.M.
#3: Journal: Nature / Year: 1987
Title: Three-Dimensional Structure of a Complex of Antibody with Influenza Virus Neuraminidase
Authors: Colman, P.M. / Laver, W.G. / Varghese, J.N. / Baker, A.T. / Tulloch, P.A. / Air, G.M. / Webster, R.G.
History
DepositionJan 21, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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.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_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_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_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
Revision 2.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
N: CALCIUM ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9037
Polymers91,1443
Non-polymers1,7594
Water1,24369
1
N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules

N: INFLUENZA A SUBTYPE N9 NEURAMINIDASE
L: IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,61228
Polymers364,57712
Non-polymers7,03516
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)167.000, 167.000, 124.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Atom site foot note1: RESIDUES PRO N 326, PRO N 431, PRO L 8, PRO L 95, PRO L 141, PRO H 149, PRO H 151 AND PRO H 200 ARE CIS PROLINES.
2: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9).
DetailsTHE COORDINATES OF THE CARBOHYDRATE IN THE EPITOPE CAN BE GENERATED FORM THE COORDINATES OF RESIDUES C 200A-C 200F BY APPLYING THE FOLLOWING TRANSFORMATION: 0.0 1.0 0.0 83.5 -1.0 0.0 0.0 83.5 0.0 0.0 1.0 0.0

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Components

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Protein , 1 types, 1 molecules N

#1: Protein INFLUENZA A SUBTYPE N9 NEURAMINIDASE


Mass: 43753.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: (A/whale/Maine/1/84(H13N9)) / References: UniProt: P05803, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody IGG2A-KAPPA NC41 FAB (LIGHT CHAIN)


Mass: 23722.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: EMBL: Y11589
#3: Antibody IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)


Mass: 23668.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_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]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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


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

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Non-polymers , 2 types, 70 molecules N

#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE FOLLOWING RESIDUES DIFFERS FROM THE CHEMICAL SEQUENCE: LYS H 46 WAS REFINED AS ...THE SEQUENCE OF THE FOLLOWING RESIDUES DIFFERS FROM THE CHEMICAL SEQUENCE: LYS H 46 WAS REFINED AS GLU THR H 87 WAS REFINED AS LYS VAL H 109 WAS REFINED AS LEU SER N 81 WAS REFINED AS ILE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.05 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: potassium phosphate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 2.9 Å
Details: THE COORDINATES OF THE CALCIUM ATOM ARE NOT WELL DETERMINED. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9)
RfactorNum. reflection
Rwork0.157 -
obs0.157 18737
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6401 0 115 69 6585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.6
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
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 18737 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.6

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