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- PDB-4iuf: Crystal Structure of Human TDP-43 RRM1 Domain in Complex with a S... -

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Basic information

Entry
Database: PDB / ID: 4iuf
TitleCrystal Structure of Human TDP-43 RRM1 Domain in Complex with a Single-stranded DNA
Components
  • 5'-D(*GP*TP*TP*GP*(XUA)P*GP*CP*GP*T)-3'
  • TAR DNA-binding protein 43
KeywordsTRANSCRIPTION REGULATOR/DNA / RNA Recognition Motif / RNA binding / DNA binding / splicing factor / TRANSCRIPTION REGULATOR-DNA complex / 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 non-membrane-bounded organelle / negative regulation by host of viral transcription / pre-mRNA intronic binding / response to endoplasmic reticulum stress / molecular condensate scaffold activity ...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 / molecular condensate scaffold activity / RNA splicing / negative regulation of protein phosphorylation / 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 / double-stranded DNA binding / regulation of gene expression / 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 / 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, C-terminal / TAR DNA-binding protein 43, N-terminal / TAR DNA-binding protein 43, N-terminal domain / 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 / SYNCHROTRON / SAD / Resolution: 2.752 Å
AuthorsKuo, P.H. / Doudeva, L.G. / Wang, Y.T. / Yang, W.Z. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids.
Authors: Kuo, P.H. / Chiang, C.H. / Wang, Y.T. / Doudeva, L.G. / Yuan, H.S.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: 5'-D(*GP*TP*TP*GP*(XUA)P*GP*CP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)11,8662
Polymers11,8662
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.110, 71.110, 101.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 8986.375 Da / Num. of mol.: 1 / Fragment: RRM1 Domain (UNP residues 103-179)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TARDBP, TDP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13148
#2: DNA chain 5'-D(*GP*TP*TP*GP*(XUA)P*GP*CP*GP*T)-3'


Mass: 2879.819 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.12M CH3COONH4, 0.05M Bis-Tris, 16% PEG 3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 4328 / % possible obs: 10 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.8 % / Biso Wilson estimate: 54.99 Å2 / Net I/σ(I): 43.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.554 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1059refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.752→26.336 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 1.36 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 430 10 %
Rwork0.2065 --
obs0.2116 4301 100 %
all-4328 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.2025 Å2
Refinement stepCycle: LAST / Resolution: 2.752→26.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms629 187 0 14 830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003852
X-RAY DIFFRACTIONf_angle_d0.7511182
X-RAY DIFFRACTIONf_dihedral_angle_d19.513318
X-RAY DIFFRACTIONf_chiral_restr0.038129
X-RAY DIFFRACTIONf_plane_restr0.003116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7518-3.14940.36651380.28261237X-RAY DIFFRACTION100
3.1494-3.96570.27121410.20531272X-RAY DIFFRACTION100
3.9657-26.33760.22071510.18531362X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.6151 Å / Origin y: 44.0918 Å / Origin z: 53.7003 Å
111213212223313233
T0.4483 Å20.0327 Å20.0819 Å2-0.3141 Å20.0794 Å2--0.3117 Å2
L3.78 °2-0.6184 °2-0.1846 °2-5.5737 °2-3.6986 °2--7.137 °2
S-0.0091 Å °-0.1048 Å °-0.3863 Å °0.164 Å °0.111 Å °0.1974 Å °0.2325 Å °0.1426 Å °-0.0131 Å °
Refinement TLS groupSelection details: all

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