[English] 日本語
Yorodumi
- PDB-6odg: SVQIVY, Crystal Structure of a tau protein fragment -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6odg
TitleSVQIVY, Crystal Structure of a tau protein fragment
ComponentsMicrotubule-associated protein tau
KeywordsPROTEIN FIBRIL / Amyloid / Tau / MicroED
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 / 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 / cellular response to reactive oxygen species / SH3 domain binding / microtubule cytoskeleton organization / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / 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 / 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.
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsEisenberg, D.S. / Boyer, D.R. / Sawaya, M.R. / Seidler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG0543022 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure-based inhibitors halt prion-like seeding by Alzheimer's disease-and tauopathy-derived brain tissue samples.
Authors: Seidler, P.M. / Boyer, D.R. / Murray, K.A. / Yang, T.P. / Bentzel, M. / Sawaya, M.R. / Rosenberg, G. / Cascio, D. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. ...Authors: Seidler, P.M. / Boyer, D.R. / Murray, K.A. / Yang, T.P. / Bentzel, M. / Sawaya, M.R. / Rosenberg, G. / Cascio, D. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. / Vinters, H.V. / Eisenberg, D.S.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated protein tau
B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)1,4162
Polymers1,4162
Non-polymers00
Water362
1
A: Microtubule-associated protein tau
B: Microtubule-associated protein tau

A: Microtubule-associated protein tau
B: Microtubule-associated protein tau

A: Microtubule-associated protein tau
B: Microtubule-associated protein tau

A: Microtubule-associated protein tau
B: Microtubule-associated protein tau

A: Microtubule-associated protein tau
B: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)7,07810
Polymers7,07810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_855x+3,y,z1
crystal symmetry operation1_955x+4,y,z1
Unit cell
Length a, b, c (Å)4.710, 37.500, 21.110
Angle α, β, γ (deg.)90.000, 92.950, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 1 - 6 / Label seq-ID: 1 - 6

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

-
Components

#1: Protein/peptide Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 707.815 Da / Num. of mol.: 2 / Fragment: UNP residues 622-627 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.32 Å3/Da / Density % sol: 6.48 %
Crystal growTemperature: 291 K / Method: batch mode
Details: 3.3 mg/mL SVQIVY, 0.667 M DL-malic acid, pH 7.0, 8% w/v PEG3350

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 1, 2017
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1→18.75 Å / Num. obs: 3392 / % possible obs: 85.2 % / Redundancy: 7.783 % / Biso Wilson estimate: 6.64 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.319 / Rrim(I) all: 0.337 / Χ2: 0.769 / Net I/σ(I): 3.57 / Num. measured all: 26400 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1-1.035.0110.7541.121860.8510.83164.8
1.03-1.055.2190.6561.642150.70.72575.7
1.05-1.085.5920.6761.742060.6930.74174.9
1.08-1.126.1630.6172.012460.7940.66987.5
1.12-1.167.4120.7111.912570.7260.75889.9
1.16-1.29.1240.6782.252340.8240.71490.3
1.2-1.247.8360.5932.42010.8520.63188.2
1.24-1.298.3390.49831890.8710.52888.7
1.29-1.358.3170.5672.812020.8290.60190.6
1.35-1.418.4970.5262.771930.9590.55887.7
1.41-1.499.6620.4684.062010.8730.49191.8
1.49-1.5810.0980.385.41940.9730.39690.7
1.58-1.697.650.3934.081370.9390.41887.3
1.69-1.838.0830.3395.481440.9230.36187.3
1.83-28.6480.3526.471420.9170.37588.8
2-2.248.8430.2847.21400.9590.30190.9
2.24-2.588.9270.4247.111090.9730.44488.6
2.58-3.167.2940.2137.03850.9970.22787.6
3.16-4.479.2980.2249.21840.9830.23887.5
4.47-18.757.9260.2238.18270.9890.23265.9

-
Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→18.75 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 37.63
RfactorNum. reflection% reflection
Rfree0.2663 339 10.03 %
Rwork0.2447 --
obs0.2469 3380 84.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 20.59 Å2 / Biso mean: 7.5434 Å2 / Biso min: 2.46 Å2
Refinement stepCycle: final / Resolution: 1→18.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms100 0 0 2 102
Biso mean---16.62 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015100
X-RAY DIFFRACTIONf_angle_d1.337136
X-RAY DIFFRACTIONf_chiral_restr0.0718
X-RAY DIFFRACTIONf_plane_restr0.0116
X-RAY DIFFRACTIONf_dihedral_angle_d20.09134
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A66X-RAY DIFFRACTION12.41TORSIONAL
12B66X-RAY DIFFRACTION12.41TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0003-1.26020.36191620.30121450161281
1.2602-18.75330.23041770.22351591176888

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more