[English] 日本語
Yorodumi
- PDB-6t4b: CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RES... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t4b
TitleCRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RESOLUTION
ComponentsTAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN / MND / NTD domain / TDP-43
Function / homology
Function and homology information


nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / RNA splicing / negative regulation of protein phosphorylation / molecular condensate scaffold activity / mRNA 3'-UTR binding / regulation of protein stability / regulation of circadian rhythm / positive regulation of insulin secretion / mRNA processing / cytoplasmic stress granule / positive regulation of protein import into nucleus / rhythmic process / regulation of gene expression / double-stranded DNA binding / regulation of apoptotic process / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / lipid binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / TAR DNA-binding protein 43, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWatanabe, T.F. / Wright, G.S.A. / Amporndanai, K. / Antonyuk, S.V. / Hasnain, S.S.
CitationJournal: Iscience / Year: 2020
Title: Purification and Structural Characterization of Aggregation-Prone Human TDP-43 Involved in Neurodegenerative Diseases.
Authors: Wright, G.S.A. / Watanabe, T.F. / Amporndanai, K. / Plotkin, S.S. / Cashman, N.R. / Antonyuk, S.V. / Hasnain, S.S.
History
DepositionOct 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TAR DNA-binding protein 43
C: TAR DNA-binding protein 43
E: TAR DNA-binding protein 43
G: TAR DNA-binding protein 43
I: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,86010
Polymers44,3805
Non-polymers4805
Water4,197233
1
A: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9722
Polymers8,8761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9722
Polymers8,8761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9722
Polymers8,8761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9722
Polymers8,8761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: TAR DNA-binding protein 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9722
Polymers8,8761
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.637, 95.224, 157.558
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
TAR DNA-binding protein 43 / / TDP-43


Mass: 8875.903 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Production host: Escherichia coli (E. coli) / Variant (production host): BL52 / References: UniProt: Q13148
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: needle like
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium bromide, 0.1M Bis-Tris propane 6.5, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.55→78.9 Å / Num. obs: 16549 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.156 / Net I/σ(I): 5.7
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1212 / CC1/2: 0.549 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mdi

5mdi


Resolution: 2.55→78.9 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.582 / ESU R Free: 0.307
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 925 5.3 %RANDOM
Rwork0.2245 ---
obs0.2265 16549 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.39 Å2 / Biso mean: 46.148 Å2 / Biso min: 18 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å20 Å20 Å2
2---2.04 Å20 Å2
3----2.33 Å2
Refinement stepCycle: final / Resolution: 2.55→78.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 25 235 3284
Biso mean--94.12 43.37 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133127
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172805
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.6534279
X-RAY DIFFRACTIONr_angle_other_deg2.3091.5736510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.67322.011179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95815476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0341527
X-RAY DIFFRACTIONr_chiral_restr0.0510.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023568
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02637
X-RAY DIFFRACTIONr_mcbond_it2.0034.9471559
X-RAY DIFFRACTIONr_mcbond_other2.0014.9451558
X-RAY DIFFRACTIONr_mcangle_it3.667.4051941
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 56 -
Rwork0.336 1212 -
all-1268 -
obs--99.76 %

+
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