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- PDB-6t4b: CRYSTAL STRUCTURE OF HUMAN TDP-43 N-TERMINAL DOMAIN AT 2.55 A RES... -

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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 membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / intracellular membraneless organelle / negative regulation of protein phosphorylation / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing / response to endoplasmic reticulum stress / mRNA 3'-UTR binding / molecular condensate scaffold activity / regulation of circadian rhythm / positive regulation of insulin secretion / regulation of protein stability / positive regulation of protein import into nucleus / mRNA processing / cytoplasmic stress granule / 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 / chromatin / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
TAR DNA-binding protein 43, N-terminal / : / TAR DNA-binding protein 43, N-terminal domain / TAR DNA-binding protein 43, C-terminal / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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

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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: 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

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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

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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 %

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