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- PDB-4glr: Structure of the anti-ptau Fab (pT231/pS235_1) in complex with ph... -

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Basic information

Entry
Database: PDB / ID: 4glr
TitleStructure of the anti-ptau Fab (pT231/pS235_1) in complex with phosphoepitope pT231/pS235
Components
  • anti-ptau heavy chain
  • anti-ptau light chain
  • phospho-peptide
KeywordsIMMUNE SYSTEM / IgG1 Fab / anti-ptau antibody / phosphorylated tau peptide / phosphorylation
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding ...plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / microtubule lateral binding / axonal transport / tubulin complex / positive regulation of protein localization to synapse / negative regulation of tubulin deacetylation / phosphatidylinositol bisphosphate binding / generation of neurons / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / regulation of chromosome organization / central nervous system neuron development / intracellular distribution of mitochondria / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / microtubule polymerization / negative regulation of mitochondrial membrane potential / dynactin binding / regulation of microtubule polymerization / apolipoprotein binding / main axon / protein polymerization / axolemma / glial cell projection / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of mitochondrial fission / neurofibrillary tangle assembly / positive regulation of axon extension / regulation of cellular response to heat / Activation of AMPK downstream of NMDARs / synapse assembly / positive regulation of superoxide anion generation / regulation of long-term synaptic depression / positive regulation of protein localization / cellular response to brain-derived neurotrophic factor stimulus / supramolecular fiber organization / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / somatodendritic compartment / axon cytoplasm / astrocyte activation / stress granule assembly / phosphatidylinositol binding / nuclear periphery / regulation of microtubule cytoskeleton organization / protein phosphatase 2A binding / cellular response to reactive oxygen species / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / synapse organization / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / SH3 domain binding / response to lead ion / microtubule cytoskeleton organization / memory / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / cellular response to heat / microtubule cytoskeleton / cell body / actin binding / growth cone / double-stranded DNA binding / protein-macromolecule adaptor activity / microtubule binding / dendritic spine / sequence-specific DNA binding / amyloid fibril formation / microtubule / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / 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
PHOSPHATE ION / Microtubule-associated protein tau
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTu, C. / Mosyak, L. / Bard, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: An Ultra-specific Avian Antibody to Phosphorylated Tau Protein Reveals a Unique Mechanism for Phosphoepitope Recognition.
Authors: Shih, H.H. / Tu, C. / Cao, W. / Klein, A. / Ramsey, R. / Fennell, B.J. / Lambert, M. / Ni Shuilleabhain, D. / Autin, B. / Kouranova, E. / Laxmanan, S. / Braithwaite, S. / Wu, L. / Ait-Zahra, ...Authors: Shih, H.H. / Tu, C. / Cao, W. / Klein, A. / Ramsey, R. / Fennell, B.J. / Lambert, M. / Ni Shuilleabhain, D. / Autin, B. / Kouranova, E. / Laxmanan, S. / Braithwaite, S. / Wu, L. / Ait-Zahra, M. / Milici, A.J. / Dumin, J.A. / Lavallie, E.R. / Arai, M. / Corcoran, C. / Paulsen, J.E. / Gill, D. / Cunningham, O. / Bard, J. / Mosyak, L. / Finlay, W.J.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Oct 2, 2013Group: Source and taxonomy
Revision 1.4Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phospho-peptide
B: phospho-peptide
H: anti-ptau heavy chain
I: anti-ptau light chain
J: anti-ptau heavy chain
K: anti-ptau light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8568
Polymers95,6666
Non-polymers1902
Water12,881715
1
A: phospho-peptide
H: anti-ptau heavy chain
I: anti-ptau light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9284
Polymers47,8333
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-44 kcal/mol
Surface area19690 Å2
MethodPISA
2
B: phospho-peptide
J: anti-ptau heavy chain
K: anti-ptau light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9284
Polymers47,8333
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-47 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.5, 216.5, 70.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide phospho-peptide


Mass: 2048.260 Da / Num. of mol.: 2 / Fragment: phospho-peptide / Source method: obtained synthetically
Details: This sequence occurs naturally in humans, except the C-terminus Cysteine
Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS
#2: Antibody anti-ptau heavy chain


Mass: 23609.414 Da / Num. of mol.: 2 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody anti-ptau light chain


Mass: 22175.260 Da / Num. of mol.: 2 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 mM NH4H2PO4, 40% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2011 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 81511 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10 % / Biso Wilson estimate: 31.54 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 4.1 / Num. unique all: 11379 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.11.1refinement
PROCESSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3GJE, 3MA9

3gje

3ma9


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.9302 / SU R Cruickshank DPI: 0.131 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 4014 5.01 %RANDOM
Rwork0.1795 ---
obs0.1809 80083 96.53 %-
Displacement parametersBiso mean: 40.85 Å2
Baniso -1Baniso -2Baniso -3
1--6.9441 Å20 Å20 Å2
2--9.6239 Å20 Å2
3----2.6797 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 10 715 7233
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016781HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.169298HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2192SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes126HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it6781HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion15.76
X-RAY DIFFRACTIONt_chiral_improper_torsion925SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7989SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2292 239 5.08 %
Rwork0.2141 4467 -
all0.2149 4706 -
obs-4706 96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67630.14640.17622.0106-1.0460.7019-0.0081-0.07290.15620.0950.08270.0124-0.008-0.0908-0.0746-0.11870.0130.02480.0090.0039-0.017-22.382663.1674-30.6908
20.4824-0.56390.12282.3738-0.93880.89630.0556-0.01790.11560.4037-0.08390.0635-0.29390.09550.0283-0.0315-0.01550.0228-0.0319-0.0226-0.0822-17.397462.7-13.9597
30.7149-0.5394-0.33424.24891.15110.7770.0698-0.0827-0.1148-0.3171-0.0361-0.0250.06010.1087-0.0337-0.01990.0566-0.0599-0.01720.0059-0.1424-16.624923.85384.2165
40.4744-0.6799-0.19273.20621.27660.7221-0.0451-0.0027-0.14820.5660.02220.12230.4329-0.03660.02290.10640.0311-0.0064-0.05710.0429-0.1334-22.315124.520621.2806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|215 }H1 - 215
2X-RAY DIFFRACTION2{ I|3 - I|209 }I3 - 209
3X-RAY DIFFRACTION3{ J|1 - J|214 }J1 - 214
4X-RAY DIFFRACTION4{ K|3 - K|209 }K3 - 209

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