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

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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 / homologyImmunoglobulin-like domain / Classical antibody-mediated complement activation / Glycoside hydrolase, family 34 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Sialidase, Influenza viruses A/B / Immunoglobulin-like domain superfamily / Sialidase superfamily / Neuraminidase / Immunoglobulin V-set domain ...Immunoglobulin-like domain / Classical antibody-mediated complement activation / Glycoside hydrolase, family 34 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Sialidase, Influenza viruses A/B / Immunoglobulin-like domain superfamily / Sialidase superfamily / Neuraminidase / Immunoglobulin V-set domain / Ig-like domain profile. / Initial triggering of complement / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Cell surface interactions at the vascular wall / FCGR activation / Regulation of actin dynamics for phagocytic cup formation / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / CD22 mediated BCR regulation / Regulation of Complement cascade / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Immunoglobulin subtype / immunoglobulin production / exo-alpha-sialidase / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->8)-sialidase activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / viral budding from plasma membrane / positive regulation of B cell activation / phagocytosis, engulfment / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / immune response / external side of plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / defense response to bacterium / innate immune response / extracellular space / integral component of membrane / metal ion binding / Ig kappa chain V-V region HP 93G7 / Ig heavy chain V region 3 / Neuraminidase / gb:501094:
Function and homology information
Specimen sourceMus musculus (house mouse)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.5 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 21, 1997 / Release: May 13, 1998
RevisionDateData content typeGroupProviderType
1.0May 13, 1998Structure modelrepositoryInitial release
1.1Mar 21, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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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)70,15913
Polyers68,3343
Non-polymers1,82610
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)280,63752
Polyers273,33412
Non-polymers7,30340
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
γ
α
β
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-MI 4 2 2

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Components

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Protein/peptide , 3 types, 3 molecules NHL

#1: Protein/peptide NEURAMINIDASE /


Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: N9, A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase
#2: Protein/peptide 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: (gene. exp.) Mus musculus (house mouse) / Genus: Mus / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01749*PLUS
#3: Protein/peptide 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: (gene. exp.) Mus musculus (house mouse) / Genus: Mus / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01645*PLUS

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Non-polymers , 5 types, 10 molecules

#4: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 3 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6
#6: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6
#7: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Formula: Ca / Calcium

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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 / Density percent sol: 7 %
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 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
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: PHOTON FACTORY / Detector: IMAGE PLATE / Collection date: Jul 1, 1995
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / Number obs: 29660 / Observed criterion sigma I: 2 / Rmerge I obs: 0.118 / Percent possible obs: 68
Reflection shellHighest resolution: 2.5 Å / Lowest resolution: 2.6 Å / Percent possible all: 4
Reflection
*PLUS
Number measured all: 86319
Reflection shell
*PLUS
Percent possible obs: 4

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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
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NMC
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / Sigma F: 2
Least-squares processR factor R free: 0.27 / R factor R work: 0.2 / R factor obs: 0.2 / Highest resolution: 2.5 Å / Lowest resolution: 7 Å / Number reflection obs: 27957 / Percent reflection R free: 1 / Percent reflection obs: 8
Refine analyzeLuzzati d res low obs: 5 Å
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 4800 / Nucleic acid: 0 / Ligand: 112 / Solvent: 0 / Total: 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
Refine
*PLUS
Sigma I: 2

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