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- PDB-5dmg: X-RAY STRUCTURE OF THE FAB FRAGMENT OF THE ANTI TAU ANTIBODY RB86... -

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Basic information

Entry
Database: PDB / ID: 5dmg
TitleX-RAY STRUCTURE OF THE FAB FRAGMENT OF THE ANTI TAU ANTIBODY RB86 IN COMPLEX WITH THE PHOSPHORYLATED TAU PEPTIDE (416-430)
Components
  • Microtubule-associated protein
  • RB86 antibody Fab fragment heavy chain
  • RB86 antibody Fab fragment light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / FAB FRAGMENT / TAU PROTEIN / Tau-pSER422 / Tau-pSER422 COMPLEX
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / apolipoprotein binding / glial cell projection / negative regulation of mitochondrial membrane potential / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / tubulin binding / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion
Similarity search - Function
: / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Microtubule-associated protein / Microtubule-associated protein tau
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenz, J. / Lorenz, S. / Georges, G. / Jochner, A. / Goepfert, U. / Grueninger, F. / Bujotzek, A.
CitationJournal: Mabs / Year: 2016
Title: VH-VL orientation prediction for antibody humanization candidate selection: A case study.
Authors: Bujotzek, A. / Lipsmeier, F. / Harris, S.F. / Benz, J. / Kuglstatter, A. / Georges, G.
History
DepositionSep 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
H: RB86 antibody Fab fragment heavy chain
L: RB86 antibody Fab fragment light chain
C: RB86 antibody Fab fragment heavy chain
D: RB86 antibody Fab fragment light chain
E: RB86 antibody Fab fragment heavy chain
F: RB86 antibody Fab fragment light chain
Z: Microtubule-associated protein
P: Microtubule-associated protein
X: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)141,5249
Polymers141,5249
Non-polymers00
Water4,972276
1
H: RB86 antibody Fab fragment heavy chain
L: RB86 antibody Fab fragment light chain
P: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RB86 antibody Fab fragment heavy chain
D: RB86 antibody Fab fragment light chain
Z: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RB86 antibody Fab fragment heavy chain
F: RB86 antibody Fab fragment light chain
X: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.510, 163.053, 70.926
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody RB86 antibody Fab fragment heavy chain


Mass: 21976.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody RB86 antibody Fab fragment light chain


Mass: 23542.150 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Microtubule-associated protein


Mass: 1655.716 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: B4DSE3, UniProt: P10636*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: Lithium sulfate, Sodium acetate, pH 4.5 PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.5→46.61 Å / Num. all: 49616 / Num. obs: 49616 / % possible obs: 99.9 % / Redundancy: 3.46 % / Rsym value: 0.08 / Net I/σ(I): 9.73
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.32 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.17 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house Fab fragment

Resolution: 2.5→46.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 23.79 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26292 2509 5.1 %RANDOM
Rwork0.20978 ---
obs0.21246 47075 99.88 %-
Displacement parametersBiso mean: 39.731 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-0.63 Å2
2--1.08 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9557 0 0 276 9833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.029780
X-RAY DIFFRACTIONr_bond_other_d0.0010.029070
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.95713352
X-RAY DIFFRACTIONr_angle_other_deg0.6813.00320971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24251264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8724.783345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.826151520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5921527
X-RAY DIFFRACTIONr_chiral_restr0.0610.21569
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022093
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 189 -
Rwork0.356 3454 -
obs--99.78 %

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