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- PDB-1zan: Crystal structure of anti-NGF AD11 Fab -

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Basic information

Entry
Database: PDB / ID: 1zan
TitleCrystal structure of anti-NGF AD11 Fab
Components
  • Fab AD11 Heavy Chain
  • Fab AD11 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Fab
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Ig heavy chain Mem5 / LOC500183 protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCovaceuszach, S. / Cattaneo, A. / Cassetta, A. / Lamba, D.
Citation
Journal: J Mol Biol / Year: 2008
Title: Dissecting NGF interactions with TrkA and p75 receptors by structural and functional studies of an anti-NGF neutralizing antibody.
Authors: Sonia Covaceuszach / Alberto Cassetta / Petr V Konarev / Stefania Gonfloni / Rainer Rudolph / Dmitri I Svergun / Doriano Lamba / Antonino Cattaneo /
Abstract: The anti-nerve growth factor (NGF) monoclonal antibody alphaD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly ...The anti-nerve growth factor (NGF) monoclonal antibody alphaD11 is a potent antagonist that neutralizes the biological functions of its antigen in vivo. NGF antagonism is expected to be a highly effective and safe therapeutic approach in many pain states. A comprehensive functional and structural analysis of alphaD11 monoclonal antibody was carried out, showing its ability to neutralize NGF binding to either tropomyosine receptor kinase A (TrkA) or p75 receptors. The 3-D structure of the alphaD11 Fab fragment was solved at 1.7 A resolution. A computational docking model of the alphaD11 Fab-NGF complex, based on epitope mapping using a pool of 44 NGF mutants and experimentally validated by small-angle X-ray scattering, provided the structural basis for identifying the residues involved in alphaD11 Fab binding. The present study pinpoints loop II of NGF to be an important structural determinant for NGF biological activity mediated by TrkA receptor.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Purification, crystallization, X-ray diffraction analysis and phasing of a Fab fragment of monoclonal neuroantibody AD11 against nerve growth factor.
Authors: Covaceuszach, S. / Cassetta, A. / Cattaneo, A. / Lamba, D.
History
DepositionApr 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab AD11 Light Chain
H: Fab AD11 Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9253
Polymers46,8902
Non-polymers351
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-34 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.801, 69.354, 64.104
Angle α, β, γ (deg.)90.00, 117.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab AD11 Light Chain


Mass: 23340.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell (production host): Hybridoma / Production host: Rattus norvegicus (Norway rat) / Keywords: Light Chain / References: UniProt: Q4KM66
#2: Antibody Fab AD11 Heavy Chain


Mass: 23549.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell (production host): Hybridoma / Production host: Rattus norvegicus (Norway rat) / Keywords: Heavy Chain / References: UniProt: P84751
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% Peg4000, 600mM NaCl, 100mM BTP, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2001 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→29.64 Å / Num. all: 47951 / Num. obs: 47951 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.058 / Net I/σ(I): 5.8
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 3198 / Rsym value: 0.278 / % possible all: 78.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CIC

1cic


Resolution: 1.7→17 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 4839 -Random
Rwork0.196 ---
all0.196 47951 --
obs0.196 47950 97 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.18 Å26.74 Å2-3.56 Å2
2--0 Å20.13 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 1 404 3631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.315 688 -
Rwork0.245 --
obs-6212 84.3 %

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