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- PDB-1nmb: THE STRUCTURE OF A COMPLEX BETWEEN THE NC10 ANTIBODY AND INFLUENZ... -

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Entry
Database: PDB / ID: 1nmb
TitleTHE STRUCTURE OF A COMPLEX BETWEEN THE NC10 ANTIBODY AND INFLUENZA VIRUS NEURAMINIDASE AND COMPARISON WITH THE OVERLAPPING BINDING SITE OF THE NC41 ANTIBODY
Components
  • (FAB NC10) x 2
  • N9 NEURAMINIDASE
KeywordsCOMPLEX (HYDROLASE/IMMUNOGLOBULIN) / COMPLEX (HYDROLASE-IMMUNOGLOBULIN) / COMPLEX (HYDROLASE-IMMUNOGLOBULIN) complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMalby, R.L. / Tulip, W.R. / Colman, P.M.
Citation
Journal: Structure / Year: 1994
Title: The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody
Authors: Malby, R.L. / Tulip, W.R. / Harley, V.R. / McKimm-Breschkin, J.L. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#1: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1989
Title: Three-Dimensional Structures of Influenza Virus Neuraminidase-Antibody Complexes
Authors: Colman, P.M. / Tulip, W.R. / Varghese, J.N. / Tulloch, P.A. / Baker, A.T. / Laver, W.G. / Air, G.M. / Webster, R.G.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1989
Title: Crystal Structure 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: Biochemistry / Year: 1994
Title: N9 Neuraminidase Complexes with Antibodies Nc41 and Nc10: Empirical Free Energy Calculations Capture Specificity Trends Observed with Mutant Binding Data
Authors: Tulip, W.R. / Harley, V.R. / Webster, R.G. / Novotny, J.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Crystal Structure of the Influenza Virus N9 Neuraminidase-Nc41 Complex
Authors: Tulip, W.R. / Varghese, J.N. / Laver, W.G. / Webster, R.G. / Colman, P.M.
History
DepositionJan 17, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 12, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_biol / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _pdbx_database_status.process_site ..._chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_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 / _database_PDB_caveat.text / _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.ptnr1_symmetry / _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
N: N9 NEURAMINIDASE
L: FAB NC10
H: FAB NC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7137
Polymers77,9953
Non-polymers1,7184
Water1,49583
1
N: N9 NEURAMINIDASE
L: FAB NC10
H: FAB NC10
hetero molecules

N: N9 NEURAMINIDASE
L: FAB NC10
H: FAB NC10
hetero molecules

N: N9 NEURAMINIDASE
L: FAB NC10
H: FAB NC10
hetero molecules

N: N9 NEURAMINIDASE
L: FAB NC10
H: FAB NC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,85228
Polymers311,98212
Non-polymers6,87016
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area36290 Å2
ΔGint-12 kcal/mol
Surface area84170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.400, 169.400, 156.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Atom site foot note1: CIS PROLINE - PRO N 326 / 2: CIS PROLINE - PRO N 431 / 3: CIS PROLINE - PRO L 95

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Components

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Protein , 1 types, 1 molecules N

#1: Protein N9 NEURAMINIDASE


Mass: 52442.445 Da / Num. of mol.: 1 / Mutation: WILD TYPE / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / References: UniProt: P05803, exo-alpha-sialidase

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Antibody , 2 types, 2 molecules LH

#2: Antibody FAB NC10


Mass: 12129.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM MONOCLONAL MURINE ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: GenBank: 501094
#3: Antibody FAB NC10


Mass: 13423.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM MONOCLONAL MURINE ANTIBODY / Source: (natural) Mus musculus (house mouse) / References: GenBank: 501094

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Sugars , 2 types, 3 molecules

#4: 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-ROHGlycam 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
[][D-1-deoxy-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-Glcp]{}}}}LINUCSPDB-CARE
#5: 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

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Non-polymers , 2 types, 84 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details83 SOLVENT ATOMS AND 1 CALCIUM ATOM INCLUDED IN MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlFab1drop
21.7 Mpotassium phosphate1drop
31.9 Mpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 31862 / Observed criterion σ(F): 2 / Num. measured all: 176473 / Rmerge(I) obs: 0.095

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2
Details: THE WHOLE OF THE CONSTANT MODULE OF THE FAB (CL AND CH1) IS NOT OBSERVED IN ELECTRON DENSITY MAPS AND IS PRESUMABLY DISORDERED. THE IDENTITY OF THR L 7 IS IN QUESTION AND IT COULD BE PRO. ...Details: THE WHOLE OF THE CONSTANT MODULE OF THE FAB (CL AND CH1) IS NOT OBSERVED IN ELECTRON DENSITY MAPS AND IS PRESUMABLY DISORDERED. THE IDENTITY OF THR L 7 IS IN QUESTION AND IT COULD BE PRO. THEREFORE IT IS ASSIGNED AN OCCUPANCY OF 0.0.
RfactorNum. reflection
Rwork0.21 -
obs0.21 31862
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 112 83 5054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2
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

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