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- PDB-5mp5: Crystal structure of DC8E8 Fab in the complex with a 14-mer tau p... -

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Basic information

Entry
Database: PDB / ID: 5mp5
TitleCrystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 6.5
Components
  • Microtubule-associated protein tauTau protein
  • antibody Fab heavy chain
  • antibody Fab light chain
KeywordsIMMUNE SYSTEM / Antibody Fab / complex / tau protein
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 / lipoprotein particle binding / 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 / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / apolipoprotein binding / 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 / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / 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 / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / SH3 domain binding / cellular response to reactive oxygen species / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / protein-macromolecule adaptor activity / single-stranded DNA binding / cell-cell signaling / cellular response to heat / cell body / actin binding / growth cone / protein-folding chaperone binding / double-stranded DNA binding / microtubule binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / neuron projection / nuclear speck / membrane raft / axon / negative regulation of gene expression / dendrite / neuronal cell body / DNA damage response / protein kinase binding / enzyme binding / mitochondrion / DNA binding
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 tau
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsSkrabana, R. / Novak, M.
CitationJournal: To be published
Title: Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 6.5
Authors: Skrabana, R. / Novak, M.
History
DepositionDec 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Derived calculations / Category: pdbx_data_processing_status / struct_conn
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody Fab heavy chain
B: antibody Fab light chain
C: antibody Fab heavy chain
D: antibody Fab light chain
E: antibody Fab heavy chain
F: antibody Fab light chain
H: antibody Fab heavy chain
I: Microtubule-associated protein tau
J: Microtubule-associated protein tau
K: Microtubule-associated protein tau
L: antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)195,84811
Polymers195,84811
Non-polymers00
Water2,216123
1
A: antibody Fab heavy chain
B: antibody Fab light chain
K: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,3303
Polymers49,3303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-29 kcal/mol
Surface area19550 Å2
MethodPISA
2
C: antibody Fab heavy chain
D: antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,8582
Polymers47,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23 kcal/mol
Surface area19520 Å2
MethodPISA
3
E: antibody Fab heavy chain
F: antibody Fab light chain
I: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)49,3303
Polymers49,3303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area19450 Å2
MethodPISA
4
H: antibody Fab heavy chain
J: Microtubule-associated protein tau
L: antibody Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,3303
Polymers49,3303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-26 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.750, 82.120, 89.040
Angle α, β, γ (deg.)92.350, 95.360, 89.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23H
14B
24D
15B
25F
16B
26L
17C
27E
18C
28H
19D
29F
110D
210L
111E
211H
112F
212L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PCAPCAARGARGAA1 - 2201 - 220
21PCAPCAARGARGCC1 - 2201 - 220
12PCAPCAPROPROAA1 - 2191 - 219
22PCAPCAPROPROEE1 - 2191 - 219
13PCAPCAARGARGAA1 - 2201 - 220
23PCAPCAARGARGHG1 - 2201 - 220
14ASPASPARGARGBB1 - 2161 - 216
24ASPASPARGARGDD1 - 2161 - 216
15ASPASPASNASNBB1 - 2151 - 215
25ASPASPASNASNFF1 - 2151 - 215
16ASPASPARGARGBB1 - 2161 - 216
26ASPASPARGARGLK1 - 2161 - 216
17PCAPCAPROPROCC1 - 2191 - 219
27PCAPCAPROPROEE1 - 2191 - 219
18PCAPCAARGARGCC1 - 2201 - 220
28PCAPCAARGARGHG1 - 2201 - 220
19ASPASPASNASNDD1 - 2151 - 215
29ASPASPASNASNFF1 - 2151 - 215
110ASPASPGLUGLUDD1 - 2181 - 218
210ASPASPGLUGLULK1 - 2181 - 218
111PCAPCAVALVALEE1 - 2181 - 218
211PCAPCAVALVALHG1 - 2181 - 218
112ASPASPASNASNFF1 - 2151 - 215
212ASPASPASNASNLK1 - 2151 - 215

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Antibody
antibody Fab heavy chain


Mass: 23685.529 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
antibody Fab light chain


Mass: 24172.787 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Microtubule-associated protein tau / Tau protein / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1471.722 Da / Num. of mol.: 3 / Fragment: UNP Residues 615-628 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.849
11-H, K, -L20.151
ReflectionResolution: 2.31→34.5 Å / Num. obs: 64648 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 2.095 % / Biso Wilson estimate: 39.915 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.86
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.4-2.462.0470.3382.540.706196.4
2.46-2.532.1080.2853.060.773196.8
2.53-2.62.10.2383.680.837197.1
2.6-2.682.110.2014.40.87196.6
2.68-2.772.1060.1575.620.912197
2.77-2.872.1040.1236.930.945197.2
2.87-2.982.1010.0988.590.967197.3
2.98-3.12.1060.07611.080.981196.8
3.1-3.242.0990.06313.680.986196.6
3.24-3.392.0960.04517.440.992196.8
3.39-3.582.0990.03621.650.995196.6
3.58-3.792.0910.03223.60.996197.1
3.79-4.062.0950.0325.70.997196.7
4.06-4.382.0930.02430.330.998196.8
4.38-4.82.1010.02132.790.998196
4.8-5.372.1010.02233.170.998196.3
5.37-6.22.090.02629.510.997194.6
6.2-7.592.0850.02528.810.998195.8
7.59-10.732.0730.01640.920.999195.9
10.73-34.52.0550.01843.580.999187.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.31→34.5 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.849 / SU B: 9.804 / SU ML: 0.246 / SU R Cruickshank DPI: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2765 3165 4.9 %RANDOM
Rwork0.2348 ---
obs0.2368 61485 85.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.73 Å2 / Biso mean: 37.366 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1-5.74 Å26.2 Å2-3.88 Å2
2---7.12 Å2-1.54 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 2.31→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13382 0 0 123 13505
Biso mean---28.58 -
Num. residues----1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213739
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212401
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.94618703
X-RAY DIFFRACTIONr_angle_other_deg1.314328740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94651752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57624.241514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131546
X-RAY DIFFRACTIONr_chiral_restr0.0740.22108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02115443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023037
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A217000.07
12C217000.07
21A215940.08
22E215940.08
31A218000.07
32H218000.07
41B218680.08
42D218680.08
51B218480.08
52F218480.08
61B221680.07
62L221680.07
71C217320.07
72E217320.07
81C218140.07
82H218140.07
91D217480.07
92F217480.07
101D226340.06
102L226340.06
111E215740.07
112H215740.07
121F220580.06
122L220580.06
LS refinement shellResolution: 2.307→2.367 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20

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