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- PDB-2aeq: An epidemiologically significant epitope of a 1998 influenza viru... -

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Basic information

Entry
Database: PDB / ID: 2aeq
TitleAn epidemiologically significant epitope of a 1998 influenza virus neuraminidase forms a highly hydrated interface in the NA-antibody complex.
Components
  • FAB heavy chainFragment antigen-binding
  • FAB light chainFragment antigen-binding
  • neuraminidase
KeywordsHYDROLASE/IMMUNE SYSTEM / INFLUENZA VIRUS NEURAMINIDASE-FAB COMPLEX / HYDROLASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


immunoglobulin complex / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / blood microparticle / membrane => GO:0016020 ...immunoglobulin complex / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / immunoglobulin mediated immune response / viral budding from plasma membrane / antigen binding / blood microparticle / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion 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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 heavy chain Mem5 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVenkatramani, L. / Bochkarev, A. / Air, G.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: An Epidemiologically Significant Epitope of a 1998 Human Influenza Virus Neuraminidase Forms a Highly Hydrated Interface in the NA-Antibody Complex
Authors: Venkatramani, L. / Bochkareva, E. / Lee, J.T. / Gulati, U. / Laver, W.G. / Bochkarev, A. / Air, G.M.
History
DepositionJul 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: neuraminidase
L: FAB light chain
H: FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,20714
Polymers90,9383
Non-polymers2,26911
Water0
1
A: neuraminidase
L: FAB light chain
H: FAB heavy chain
hetero molecules

A: neuraminidase
L: FAB light chain
H: FAB heavy chain
hetero molecules

A: neuraminidase
L: FAB light chain
H: FAB heavy chain
hetero molecules

A: neuraminidase
L: FAB light chain
H: FAB heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,83056
Polymers363,75412
Non-polymers9,07644
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Unit cell
Length a, b, c (Å)159.753, 159.753, 104.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein neuraminidase /


Mass: 43867.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: A-MEMPHIS-31-98
References: UniProt: Q80DL0, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Antibody FAB light chain / Fragment antigen-binding


Mass: 23779.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma 6H3.2A11 (Mem5) / Source: (natural) Mus musculus (house mouse)
#3: Antibody FAB heavy chain / Fragment antigen-binding


Mass: 23292.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma 6H3.2A11 (Mem5) / Source: (natural) Mus musculus (house mouse) / References: UniProt: P84751*PLUS
#4: 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.: 7
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
#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.: 4
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

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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: 3.5 Å3/Da / Density % sol: 64.2 %
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 23223 / % possible obs: 93.7 % / Redundancy: 2.96 % / Rsym value: 0.114 / Net I/σ(I): 10.04
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 3.28 / Rsym value: 0.339 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NN2, 1NCA

1nn2

1nca


Resolution: 3→19.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 118997.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.312 2313 10 %RANDOM
Rwork0.267 ---
obs0.267 23223 84.6 %-
all-48044 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.71 Å20 Å20 Å2
2---2.71 Å20 Å2
3---5.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4758 0 142 0 4900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 343 9.7 %
Rwork0.336 3203 -
obs--79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM

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