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- PDB-5mp3: Crystal structure of DC8E8 Fab in the complex with a 30-mer tau p... -

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Basic information

Entry
Database: PDB / ID: 5mp3
TitleCrystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5
Components
  • ENSMUSG00000076577 protein
  • Igh protein
  • Microtubule-associated protein
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 / 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 / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / immunoglobulin complex, circulating / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / immunoglobulin receptor binding / 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 / complement activation, classical pathway / astrocyte activation / antigen binding / 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 / cellular response to reactive oxygen species / microtubule cytoskeleton organization / 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 / cell body / protein-folding chaperone binding / antibacterial humoral response / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / blood microparticle / nuclear speck / neuron projection / immune response / membrane raft / axon / negative regulation of gene expression
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. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site ...: / 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. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Microtubule-associated protein / Microtubule-associated protein tau / ENSMUSG00000076577 protein / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
CitationJournal: To be published
Title: Crystal structure of DC8E8 Fab in the complex with a 30-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 1.1Nov 21, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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
H: Igh protein
L: ENSMUSG00000076577 protein
A: Igh protein
B: ENSMUSG00000076577 protein
C: Microtubule-associated protein
D: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)102,0066
Polymers102,0066
Non-polymers00
Water1,04558
1
H: Igh protein
L: ENSMUSG00000076577 protein
D: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)51,0033
Polymers51,0033
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-30 kcal/mol
Surface area19360 Å2
MethodPISA
2
A: Igh protein
B: ENSMUSG00000076577 protein
C: Microtubule-associated protein


Theoretical massNumber of molelcules
Total (without water)51,0033
Polymers51,0033
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-29 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.850, 89.890, 83.600
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
12L
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PCAPCAARGARGHA1 - 2201 - 220
21PCAPCAARGARGAC1 - 2201 - 220
12ASPASPGLUGLULB1 - 2181 - 218
22ASPASPGLUGLUBD1 - 2181 - 218

NCS ensembles :
ID
1
2

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Components

#1: Antibody Igh protein


Mass: 23685.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LC4
#2: Antibody ENSMUSG00000076577 protein


Mass: 24172.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L64
#3: Protein/peptide Microtubule-associated protein


Mass: 3144.622 Da / Num. of mol.: 2 / Fragment: UNP Residues 615-628 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A024R9Y0, UniProt: P10636*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Feb 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.912
11-h,-k,l20.088
ReflectionResolution: 2.75→44.94 Å / Num. obs: 23880 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.461 % / Biso Wilson estimate: 46.056 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.129 / Χ2: 0.958 / Net I/σ(I): 10.98 / Num. measured all: 82638 / Scaling rejects: 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.75-2.823.0730.7871.520.598198.9
2.82-2.93.2840.6821.920.665199.8
2.9-2.983.5380.5632.510.771100
2.98-3.073.6790.4023.560.876199.9
3.07-3.183.5510.3164.450.923199.9
3.18-3.293.4250.2345.840.942199.8
3.29-3.413.2030.1597.910.971199.6
3.41-3.553.250.11810.530.98199.9
3.55-3.713.3210.11710.970.982199.5
3.71-3.893.4330.10512.20.987199.9
3.89-4.13.5880.08814.550.9911100
4.1-4.353.5960.06917.940.995199.8
4.35-4.653.650.05821.20.9961100
4.65-5.023.6480.05520.830.9971100
5.02-5.53.5040.05720.30.995199.9
5.5-6.153.5330.07315.910.994199.9
6.15-7.13.5680.07614.210.9941100
7.1-8.73.7780.04123.390.9991100
8.7-12.33.7540.02637.880.9991100
12.3-44.943.6090.02341.330.999197.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.75→44.94 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.452 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 1136 4.8 %RANDOM
Rwork0.199 ---
obs0.2014 22740 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 165.55 Å2 / Biso mean: 47.15 Å2 / Biso min: 16.94 Å2
Baniso -1Baniso -2Baniso -3
1--22.17 Å2-0 Å2-7.13 Å2
2--37.66 Å20 Å2
3----15.49 Å2
Refinement stepCycle: final / Resolution: 2.75→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6773 0 0 58 6831
Biso mean---37.94 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026960
X-RAY DIFFRACTIONr_bond_other_d0.0070.026299
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9469473
X-RAY DIFFRACTIONr_angle_other_deg0.998314601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445890
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31524.225258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.057151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.421523
X-RAY DIFFRACTIONr_chiral_restr0.0880.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217829
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021538
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H132620.09
12A132620.09
21L137780.08
22B137780.08
LS refinement shellResolution: 2.745→2.817 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 74 -
Rwork0.277 1569 -
all-1643 -
obs--92.36 %

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