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- PDB-3d2w: Crystal structure of mouse TDP-43 RRM2 domain in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 3d2w
TitleCrystal structure of mouse TDP-43 RRM2 domain in complex with DNA
Components
  • DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
  • TAR DNA-binding protein 43
KeywordsDNA/RNA BINDING PROTEIN / DP-43 proteinopathy / TDP-43 inclusions / RNA recognition motif / FTLD-U / ALS / RRM / DNA-RNA BINDING PROTEIN 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 / host-mediated suppression of viral transcription / pre-mRNA intronic binding / RNA splicing / response to endoplasmic reticulum stress / mRNA 3'-UTR binding ...nuclear inner membrane organization / interchromatin granule / perichromatin fibrils / 3'-UTR-mediated mRNA destabilization / 3'-UTR-mediated mRNA stabilization / 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 apoptotic process / gene expression / amyloid fibril formation / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrion / RNA binding / 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
PHOSPHATE ION / DNA / TAR DNA-binding protein 43
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKuo, P.H. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural insights into TDP-43 in nucleic-acid binding and domain interactions
Authors: Kuo, P.H. / Doudeva, L.G. / Wang, Y.T. / Shen, C.K. / Yuan, H.S.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2833
Polymers13,1882
Non-polymers951
Water2,090116
1
A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules

A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5676
Polymers26,3774
Non-polymers1902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
2
A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules

A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules

A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules

A: TAR DNA-binding protein 43
B: DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,13412
Polymers52,7548
Non-polymers3804
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation9_455x-1/2,y,z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Unit cell
Length a, b, c (Å)41.283, 87.290, 125.345
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-27-

HOH

21A-36-

HOH

31A-72-

HOH

41A-105-

HOH

51B-94-

HOH

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Components

#1: Protein TAR DNA-binding protein 43 / TDP-43 / RRM2 domain of mouse TDP-43


Mass: 10097.466 Da / Num. of mol.: 1 / Fragment: RRM2 motif, UNP residues 192-265
Source method: isolated from a genetically manipulated source
Details: brain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tardbp, Tdp43 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q921F2
#2: DNA chain DNA (5'-D(*DGP*DTP*DTP*DGP*DAP*DGP*DCP*DGP*DTP*DT)-3')


Mass: 3091.026 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nucleotide synthesis
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Reservoir solution containing 2M (NH4)2SO4, 0.1M phosphate-citrate, the reservoir solution contained an addition of 10% glycerol, pH4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2phosphate-citrate11
3glycerol11
4HOH11
5(NH4)2SO412
6phosphate-citrate12
7glycerol12
8HOH12

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 23, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→25.46 Å / Num. all: 13674 / Num. obs: 13854 / % possible obs: 98.7 % / Observed criterion σ(F): 1.87 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.51 / Num. unique all: 1310 / Rsym value: 0.32 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WF0

1wf0


Resolution: 1.65→25.46 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.912 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24515 1041 7.6 %RANDOM
Rwork0.20728 ---
obs0.21031 12633 98.74 %-
all-12633 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.201 Å
Refinement stepCycle: LAST / Resolution: 1.65→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 186 5 116 868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2572.2531095
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.855571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7622528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7351595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.406152
X-RAY DIFFRACTIONr_chiral_restr0.0760.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02528
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2331
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2517
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.5363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4842574
X-RAY DIFFRACTIONr_scbond_it1.6763527
X-RAY DIFFRACTIONr_scangle_it2.5674.5521
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.651→1.694 Å / Rfactor Rfree error: 0.11 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 66 -
Rwork0.247 892 -
obs-892 95.99 %

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