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- PDB-1a14: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -

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Basic information

Entry
Database: PDB / ID: 1a14
TitleCOMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 5 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE
Components
  • NC10 FV (HEAVY CHAIN)
  • NC10 FV (LIGHT CHAIN)
  • NEURAMINIDASE
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / SINGLE-CHAIN ANTIBODY / GLYCOSYLATED PROTEIN / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


immunoglobulin production / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis ...immunoglobulin production / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / positive regulation of B cell activation / phagocytosis, recognition / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / phagocytosis, engulfment / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / complement activation, classical pathway / antigen binding / viral budding from plasma membrane / B cell receptor signaling pathway / adaptive immune response / carbohydrate metabolic process / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / host cell plasma membrane / virion membrane / extracellular space / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / : / Ig kappa chain V-V region HP 93G7 / Ig heavy chain V region 3 / Neuraminidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMalby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Three-dimensional structures of single-chain Fv-neuraminidase complexes.
Authors: Malby, R.L. / McCoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M.
#1: Journal: Proteins / Year: 1993
Title: Recombinant Antineuraminidase Single Chain Antibody: Expression, Characterization, and Crystallization in Complex with Antigen
Authors: Malby, R.L. / Caldwell, J.B. / Gruen, L.C. / Harley, V.R. / Ivancic, N. / Kortt, A.A. / Lilley, G.G. / Power, B.E. / Webster, R.G. / Colman, P.M. / Hudson, P.J.
History
DepositionDec 21, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 21, 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 / Non-polymer description / 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.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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _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_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_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_atom_id_2 / _pdbx_validate_close_contact.auth_comp_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
Revision 2.1Aug 2, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: NEURAMINIDASE
H: NC10 FV (HEAVY CHAIN)
L: NC10 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0698
Polymers68,3343
Non-polymers1,7365
Water0
1
N: NEURAMINIDASE
H: NC10 FV (HEAVY CHAIN)
L: NC10 FV (LIGHT CHAIN)
hetero molecules

N: NEURAMINIDASE
H: NC10 FV (HEAVY CHAIN)
L: NC10 FV (LIGHT CHAIN)
hetero molecules

N: NEURAMINIDASE
H: NC10 FV (HEAVY CHAIN)
L: NC10 FV (LIGHT CHAIN)
hetero molecules

N: NEURAMINIDASE
H: NC10 FV (HEAVY CHAIN)
L: NC10 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,27732
Polymers273,33412
Non-polymers6,94220
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)165.300, 165.300, 182.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody NC10 FV (HEAVY CHAIN)


Mass: 13225.504 Da / Num. of mol.: 1
Fragment: VH DOMAIN OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIVE-RESIDUE POLYPEPTIDE LINKER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01749*PLUS
#3: Antibody NC10 FV (LIGHT CHAIN)


Mass: 11384.294 Da / Num. of mol.: 1
Fragment: VL DOMAIN OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIVE-RESIDUE POLYPEPTIDE LINKER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01645*PLUS

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Protein / Non-polymers , 2 types, 2 molecules N

#1: Protein NEURAMINIDASE /


Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: N9, A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Sugars , 3 types, 4 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: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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 / 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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Details

Nonpolymer detailsTHE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE ...THE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE TO WHICH THEY ARE ATTACHED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 70 %
Crystal growMethod: vapor diffusion / pH: 6.6
Details: NC10 SCFV(5) AND N9 NA WERE MIXED TOGETHER (SCFV(5) IN FOUR-FOLD MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION ...Details: NC10 SCFV(5) AND N9 NA WERE MIXED TOGETHER (SCFV(5) IN FOUR-FOLD MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8., vapor diffusion
PH range: 6.6-6.8
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: 1 was mixed with 2 in the molar ration 1:4, and an equal volume of 3 was added.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlneuraminidase1drop1
35 mg/mlscFv(5)1drop2
41.7 Mpotassium phosphate1drop3
51.3 Mpotassium phosphate1reservoir
2phosphate-beffered saline1drop1

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: PHOTON FACTORY / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 29660 / % possible obs: 68 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.118
Reflection shellResolution: 2.5→2.6 Å / % possible all: 40
Reflection
*PLUS
Num. measured all: 86319
Reflection shell
*PLUS
% possible obs: 40 %

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Processing

Software
NameVersionClassification
WEISdata collection
PROTEINdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
PROTEINdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NMC

1nmc


Resolution: 2.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -10 %RANDOM
Rwork0.2 ---
obs0.2 27957 80 %-
Refine analyzeLuzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 112 0 4912
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_deg1.9
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOTOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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