[English] 日本語
Yorodumi
- PDB-9g13: VHH H3-2 in complex with Tau C-terminal peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g13
TitleVHH H3-2 in complex with Tau C-terminal peptide
Components
  • Isoform Tau-F of Microtubule-associated protein tau
  • VHH H3-2
KeywordsIMMUNE SYSTEM / VHH / Nanobody / Tau
Function / homology
Function and homology information


plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / negative regulation of kinase activity / regulation of long-term synaptic depression / negative regulation of tubulin deacetylation / generation of neurons / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / central nervous system neuron development / regulation of microtubule polymerization / apolipoprotein binding / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / negative regulation of mitochondrial membrane potential / glial cell projection / protein polymerization / axolemma / negative regulation of mitochondrial fission / regulation of microtubule polymerization or depolymerization / Caspase-mediated cleavage of cytoskeletal proteins / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / positive regulation of protein localization / cytoplasmic microtubule organization / stress granule assembly / supramolecular fiber organization / regulation of calcium-mediated signaling / axon cytoplasm / somatodendritic compartment / positive regulation of microtubule polymerization / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / nuclear periphery / phosphatidylinositol binding / 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 / microglial cell activation / synapse organization / Hsp90 protein binding / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / : / memory / SH3 domain binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-folding chaperone binding / single-stranded DNA binding / actin binding / cellular response to heat / protein-macromolecule adaptor activity / double-stranded DNA binding / growth cone / cell body / microtubule binding / sequence-specific DNA binding / microtubule / amyloid fibril formation / 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 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.
Similarity search - Domain/homology
Microtubule-associated protein tau
Similarity search - Component
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDupre, E. / Landrieu, I. / Danis, C. / Hanoulle, X. / Mortelecque, J.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0016 France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-01 France
CitationJournal: To Be Published
Title: VHH H3-2 in complex with Tau C-terminal peptide
Authors: Dupre, E. / Landrieu, I. / Danis, C. / Hanoulle, X. / Mortelecque, J.
History
DepositionJul 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VHH H3-2
B: Isoform Tau-F of Microtubule-associated protein tau
E: VHH H3-2
F: Isoform Tau-F of Microtubule-associated protein tau
C: VHH H3-2
D: Isoform Tau-F of Microtubule-associated protein tau
G: VHH H3-2
H: Isoform Tau-F of Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)63,6788
Polymers63,6788
Non-polymers00
Water8,467470
1
A: VHH H3-2
B: Isoform Tau-F of Microtubule-associated protein tau
C: VHH H3-2
D: Isoform Tau-F of Microtubule-associated protein tau


  • defined by author&software
  • Evidence: gel filtration
  • 31.8 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)31,8394
Polymers31,8394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-49 kcal/mol
Surface area14020 Å2
MethodPISA
2
E: VHH H3-2
F: Isoform Tau-F of Microtubule-associated protein tau
G: VHH H3-2
H: Isoform Tau-F of Microtubule-associated protein tau


  • defined by author&software
  • Evidence: gel filtration
  • 31.8 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)31,8394
Polymers31,8394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-46 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.394, 76.346, 95.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody
VHH H3-2


Mass: 14270.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide
Isoform Tau-F of Microtubule-associated protein tau / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 1648.923 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.02 Å3/Da / Density % sol: 39.09 % / Description: Hexagonal pillars
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 23% PEG-MME 2000, 0.1 M potassium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564977646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564977646 Å / Relative weight: 1
ReflectionResolution: 1.8→45.549 Å / Num. obs: 48459 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.04 / Rrim(I) all: 0.096 / Net I/σ(I): 19.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-45.519.30.0374520.9920.0170.041
1.8-1.8410.72.58628130.7211.1782.846

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Cootmodel building
Aimlessdata scaling
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.549 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.04 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2312 2348 4.851 %
Rwork0.1717 46050 -
all0.174 --
obs-48398 99.944 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.115 Å2
Baniso -1Baniso -2Baniso -3
1-0.396 Å20 Å2-0 Å2
2---0.395 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 0 470 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124341
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163912
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.8035873
X-RAY DIFFRACTIONr_angle_other_deg0.8241.7488974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.826529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82810686
X-RAY DIFFRACTIONr_dihedral_angle_6_deg1410190
X-RAY DIFFRACTIONr_chiral_restr0.1230.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
X-RAY DIFFRACTIONr_nbd_refined0.2250.2674
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23473
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22009
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.22403
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2340
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1920.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.236
X-RAY DIFFRACTIONr_nbd_other0.2010.2119
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2570.232
X-RAY DIFFRACTIONr_mcbond_it5.9323.742200
X-RAY DIFFRACTIONr_mcbond_other5.913.7412200
X-RAY DIFFRACTIONr_mcangle_it8.5676.6652737
X-RAY DIFFRACTIONr_mcangle_other8.5666.6672738
X-RAY DIFFRACTIONr_scbond_it6.5944.0442141
X-RAY DIFFRACTIONr_scbond_other6.5874.0432140
X-RAY DIFFRACTIONr_scangle_it9.3437.183134
X-RAY DIFFRACTIONr_scangle_other9.3417.1813135
X-RAY DIFFRACTIONr_lrange_it12.28349.5024831
X-RAY DIFFRACTIONr_lrange_other12.30547.3954720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.3261760.25633410.25935220.9420.96899.8580.242
1.847-1.8970.3031640.24232600.24534240.9490.9691000.223
1.897-1.9520.2591670.20732000.2133720.9580.97599.85170.186
1.952-2.0120.281880.18730540.19232430.9520.97799.96920.169
2.012-2.0780.2531620.18230230.18531860.960.97899.96860.167
2.078-2.1510.2441470.18128670.18430140.9620.9791000.168
2.151-2.2320.2481380.17428180.17729560.960.9811000.162
2.232-2.3230.2711480.18127060.18628550.9540.97999.9650.169
2.323-2.4260.211190.16526240.16727430.9720.9831000.157
2.426-2.5440.2521160.17725200.1826360.960.981000.169
2.544-2.6810.261100.17523620.17924720.9560.981000.17
2.681-2.8430.2211330.17122360.17323690.9690.9811000.17
2.843-3.0380.1861050.15321350.15522420.9780.98699.91080.155
3.038-3.280.255790.18320100.18620890.960.9811000.192
3.28-3.5920.207820.16818370.1719190.9730.9861000.181
3.592-4.0120.206750.15916930.16117680.9710.9851000.179
4.012-4.6270.181750.12514750.12715500.9820.991000.147
4.627-5.6530.197730.14412790.14613520.9820.991000.175
5.653-7.9330.249650.2129980.21410630.9690.9791000.243
7.933-45.5490.308260.2096120.2136460.9080.96998.76160.263

+
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://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