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- PDB-1nma: N9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRIC... -

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Basic information

Entry
Database: PDB / ID: 1nma
TitleN9 NEURAMINIDASE COMPLEXES WITH ANTIBODIES NC41 AND NC10: EMPIRICAL FREE-ENERGY CALCULATIONS CAPTURE SPECIFICITY TRENDS OBSERVED WITH MUTANT BINDING DATA
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-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
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: 3 Å
AuthorsTulip, W.R. / Varghese, J.N. / Colman, P.M.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Refined Crystal Structures 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.
#2: 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.
#3: 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.
History
DepositionMay 6, 1994Processing 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 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 / 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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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

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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)70,4895
Polymers69,1953
Non-polymers1,2942
Water00
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)281,95520
Polymers276,77812
Non-polymers5,1778
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)171.500, 171.500, 160.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Atom site foot note1: GLY N 248 - PRO N 249 OMEGA = 214.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO N 326
3: ARG N 327 - PRO N 328 OMEGA = 146.03 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO N 431 / 5: CIS PROLINE - PRO L 95
DetailsTHE COORDINATES OF THE CARBOHYDRATE 200A - 200F DO NOT REQUIRE TRANSFORMATION TO APPEAR AS PART OF THE EPITOPE. THIS CARBOHYDRATE IS COVALENTLY ATTACHED TO THE NEURAMINIDASE SUBUNIT WHICH IS NEIGHBORING TO THE ONE IN THIS FILE.

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Components

#1: Protein N9 NEURAMINIDASE


Mass: 43640.535 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
#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: 13424.707 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
#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-ROHGlycam 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
[][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]{}}}}}}LINUCSPDB-CARE
#5: 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
Compound detailsNEURAMINIDASE RESIDUES 458 - 468 ARE INCORRECT, ALL BEING ONE RESIDUE OUT OF REGISTER. THEY ARE NOT ...NEURAMINIDASE RESIDUES 458 - 468 ARE INCORRECT, ALL BEING ONE RESIDUE OUT OF REGISTER. THEY ARE NOT PART OF ANTIBODY BINDING SITE.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.09 %
Crystal grow
*PLUS
Method: unknown

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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
RefinementRfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 3 Å
Details: NO SOLVENT ATOMS AND NO CALCIUM ATOM. THE REFERENCE STRUCTURE FOR THE CALCIUM ATOM IS THE N9 MUTANT S370L (PDB ENTRY 2NN9).
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 86 0 4863
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_deg3.5
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
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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