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- PDB-6h06: FAB CBTAU-22.1 IN COMPLEX WITH TAU PEPTIDE V1088-5 -

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Basic information

Entry
Database: PDB / ID: 6h06
TitleFAB CBTAU-22.1 IN COMPLEX WITH TAU PEPTIDE V1088-5
Components
  • HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
  • HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
  • Microtubule-associated protein tau
KeywordsIMMUNE SYSTEM / FAB / Tau peptide / complex
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 / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression ...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 / positive regulation of protein localization to synapse / main axon / phosphatidylinositol bisphosphate binding / regulation of long-term synaptic depression / tubulin complex / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / rRNA metabolic process / axonal transport of mitochondrion / regulation of mitochondrial fission / axon development / central nervous system neuron development / intracellular distribution of mitochondria / regulation of microtubule polymerization / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / apolipoprotein binding / glial cell projection / axolemma / protein polymerization / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / neurofibrillary tangle assembly / Activation of AMPK downstream of NMDARs / synapse assembly / regulation of cellular response to heat / supramolecular fiber organization / positive regulation of protein localization / regulation of calcium-mediated signaling / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / cytoplasmic microtubule organization / axon cytoplasm / positive regulation of microtubule polymerization / stress granule assembly / phosphatidylinositol binding / regulation of microtubule cytoskeleton organization / nuclear periphery / protein phosphatase 2A binding / positive regulation of superoxide anion generation / cellular response to reactive oxygen species / astrocyte activation / Hsp90 protein binding / microglial cell activation / cellular response to nerve growth factor stimulus / response to lead ion / synapse organization / PKR-mediated signaling / protein homooligomerization / regulation of synaptic plasticity / SH3 domain binding / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / cellular response to heat / microtubule cytoskeleton / cell body / growth cone / double-stranded DNA binding / microtubule binding / protein-macromolecule adaptor activity / dendritic spine / sequence-specific DNA binding / microtubule / amyloid fibril formation / learning or memory / neuron projection / regulation of autophagy / membrane raft / axon / negative regulation of gene expression / neuronal cell body / dendrite / DNA damage response / 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
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsJuraszek, J. / Steinbacher, S.
CitationJournal: Acta Neuropathol Commun / Year: 2018
Title: Enhancement of therapeutic potential of a naturally occurring human antibody targeting a phosphorylated Ser422containing epitope on pathological tau.
Authors: van Ameijde, J. / Crespo, R. / Janson, R. / Juraszek, J. / Siregar, B. / Verveen, H. / Sprengers, I. / Nahar, T. / Hoozemans, J.J. / Steinbacher, S. / Willems, R. / Delbroek, L. / Borgers, M. ...Authors: van Ameijde, J. / Crespo, R. / Janson, R. / Juraszek, J. / Siregar, B. / Verveen, H. / Sprengers, I. / Nahar, T. / Hoozemans, J.J. / Steinbacher, S. / Willems, R. / Delbroek, L. / Borgers, M. / Dockx, K. / Van Kolen, K. / Mercken, M. / Pascual, G. / Koudstaal, W. / Apetri, A.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.country / _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
L: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
A: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
B: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
C: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
D: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
E: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
F: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
I: Microtubule-associated protein tau
G: Microtubule-associated protein tau
J: Microtubule-associated protein tau
K: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,70317
Polymers203,24312
Non-polymers4605
Water81145
1
H: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
L: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
I: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9034
Polymers50,8113
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-34 kcal/mol
Surface area20510 Å2
MethodPISA
2
A: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
B: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
K: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9955
Polymers50,8113
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-33 kcal/mol
Surface area20440 Å2
MethodPISA
3
C: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
D: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
G: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9034
Polymers50,8113
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-31 kcal/mol
Surface area20430 Å2
MethodPISA
4
E: HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1
F: HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1
J: Microtubule-associated protein tau
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9034
Polymers50,8113
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-33 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.055, 96.209, 108.984
Angle α, β, γ (deg.)90.00, 112.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
HUMAN FAB ANTIBODY FRAGMENT OF CBTAU-22.1


Mass: 23874.799 Da / Num. of mol.: 4 / Fragment: FAB ANTIBODY FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
HUMAN FAB ANTIBODY FRAGMENT OF HCBTAU-22.1


Mass: 24089.922 Da / Num. of mol.: 4 / Fragment: FAB ANTIBODY FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide
Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 2845.922 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.6 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.20 M KCl, 0.10 M Hepes/NaOH pH=7, 21.2 % (w/v) PEG 5K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.63→100.46 Å / Num. obs: 59335 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.97
Reflection shellResolution: 2.63→2.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→100.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.873 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.979 / ESU R Free: 0.346 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26963 821 1.4 %RANDOM
Rwork0.21627 ---
obs0.21701 58513 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.255 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å22.16 Å2
2---0.39 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.63→100.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13510 0 30 45 13585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01913743
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212601
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.95718720
X-RAY DIFFRACTIONr_angle_other_deg0.864329104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97651758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47723.79525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.172152121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5411569
X-RAY DIFFRACTIONr_chiral_restr0.0670.22107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115553
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023056
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_it5.2937.1237080
X-RAY DIFFRACTIONr_mcbond_other5.2927.1227079
X-RAY DIFFRACTIONr_mcangle_it7.76211.9978822
X-RAY DIFFRACTIONr_mcangle_other7.76111.9988823
X-RAY DIFFRACTIONr_scbond_it5.9457.5626663
X-RAY DIFFRACTIONr_scbond_other5.9457.5626663
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.60612.4719899
X-RAY DIFFRACTIONr_long_range_B_refined10.83331.26113568
X-RAY DIFFRACTIONr_long_range_B_other10.8331.26113567
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.63→2.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 79 -
Rwork0.362 4240 -
obs--95.51 %

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