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- PDB-4y0f: Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an ... -

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Basic information

Entry
Database: PDB / ID: 4y0f
TitleCrystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA
Components
  • DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')
  • TAR DNA-binding protein 43
KeywordsDNA BINDING PROTEIN/DNA / RNA recognition motif 1 Complex / DNA BINDING PROTEIN-DNA complex
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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...TAR DNA-binding protein 43, N-terminal / : / TAR DNA-binding protein 43, N-terminal domain / TAR DNA-binding protein 43, C-terminal / RRM (RNA recognition motif) 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / TAR DNA-binding protein 43
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.648 Å
AuthorsChiang, C.H. / Kuo, P.H. / Doudeva, L.G. / Wang, Y.T. / Yuan, H.S.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica Taiwan
National Science Council Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation
Authors: Chiang, C.H. / Grauffel, C. / Wu, L.S. / Kuo, P.H. / Doudeva, L.G. / Lim, C. / Shen, C.K. / Yuan, H.S.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Derived calculations / Experimental preparation / Category: exptl_crystal_grow / pdbx_struct_oper_list
Item: _exptl_crystal_grow.pH / _exptl_crystal_grow.pdbx_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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
B: TAR DNA-binding protein 43
C: DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')
D: DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)30,3124
Polymers30,3124
Non-polymers00
Water66737
1
A: TAR DNA-binding protein 43
C: DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,1562
Polymers15,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TAR DNA-binding protein 43
D: DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)15,1562
Polymers15,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.027, 100.027, 98.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-210-

HOH

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Components

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


Mass: 12064.745 Da / Num. of mol.: 2 / Fragment: UNP residues 101-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13148
#2: DNA chain DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')


Mass: 3091.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.12M ammonium acetate, 0.08M BIS-TRIS, pH 5.5, 20% PEG 3350
PH range: 5.5-7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.648→27.701 Å / Num. all: 8322 / Num. obs: 7991 / % possible obs: 93.63 % / Redundancy: 9.7 % / Net I/σ(I): 44.43

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IUF

4iuf


Resolution: 2.648→27.701 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2883 797 9.97 %
Rwork0.2404 --
obs0.2451 7991 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.648→27.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 289 0 37 1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021615
X-RAY DIFFRACTIONf_angle_d0.6642232
X-RAY DIFFRACTIONf_dihedral_angle_d20.486613
X-RAY DIFFRACTIONf_chiral_restr0.039244
X-RAY DIFFRACTIONf_plane_restr0.002229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6479-2.81370.39991100.2957955X-RAY DIFFRACTION74
2.8137-3.03060.33341140.30521070X-RAY DIFFRACTION82
3.0306-3.33520.36471280.27571187X-RAY DIFFRACTION90
3.3352-3.81670.31651400.23071244X-RAY DIFFRACTION95
3.8167-4.80460.24131460.2091313X-RAY DIFFRACTION98
4.8046-27.70280.24841590.2331425X-RAY DIFFRACTION99

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