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- PDB-3llh: Crystal structure of the first dsRBD of TAR RNA-binding protein 2 -

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Basic information

Entry
Database: PDB / ID: 3llh
TitleCrystal structure of the first dsRBD of TAR RNA-binding protein 2
ComponentsRISC-loading complex subunit TARBP2
KeywordsRNA BINDING PROTEIN / dsRBD / DSRM / microRNA
Function / homology
Function and homology information


regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex ...regulation of siRNA processing / regulation of miRNA processing / regulation of viral transcription / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / regulation of regulatory ncRNA processing / negative regulation of defense response to virus by host / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / global gene silencing by mRNA cleavage / RISC-loading complex / RISC complex assembly / miRNA processing / siRNA binding / pre-miRNA processing / siRNA processing / pre-mRNA binding / RISC complex / MicroRNA (miRNA) biogenesis / miRNA binding / positive regulation of viral genome replication / protein sequestering activity / negative regulation of protein kinase activity / PKR-mediated signaling / double-stranded RNA binding / regulation of translation / nuclear body / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RISC-loading complex subunit TRBP2 / TRBP2 , first double-stranded RNA binding domain / TRBP2 , second double-stranded RNA binding domain / TRBP2 , third double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain ...RISC-loading complex subunit TRBP2 / TRBP2 , first double-stranded RNA binding domain / TRBP2 , second double-stranded RNA binding domain / TRBP2 , third double-stranded RNA binding domain / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / RISC-loading complex subunit TARBP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsYamashita, S. / Kawazoe, M. / Takemoto, C. / Sekine, S. / Wakiyama, M. / Yokoyama, S.
CitationJournal: To be Published
Title: The structures of dsRBDs of human TRBP
Authors: Yamashita, S. / Nagata, T. / Kawazoe, M. / Takemoto, C. / Muto, Y. / Sekine, S. / Wakiyama, M. / Yokoyama, S.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: 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 / 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: RISC-loading complex subunit TARBP2
B: RISC-loading complex subunit TARBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9763
Polymers18,8742
Non-polymers1021
Water59433
1
A: RISC-loading complex subunit TARBP2


Theoretical massNumber of molelcules
Total (without water)9,4371
Polymers9,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RISC-loading complex subunit TARBP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5392
Polymers9,4371
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.184, 51.184, 42.828
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein RISC-loading complex subunit TARBP2 / TAR RNA-binding protein 2 / Trans-activation-responsive RNA-binding protein


Mass: 9436.872 Da / Num. of mol.: 2 / Fragment: UNP residues 22-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 6895 / Plasmid: pGEX6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15633
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.7161 Å3/Da / Density % sol: 28.326 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.44M SODIUM MALONATE pH7.0, 0.2M AMMONIUM SULFATE, 0.5% v/v ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2009 / Details: RHODIUM-COATED MIRRORS
RadiationMonochromator: ROTATED-INCLINED DOUBLE-CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 6917 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.152 / Net I/σ(I): 12.175
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.807 / Num. unique all: 680 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RC7

1rc7


Resolution: 2.14→44.33 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 749893.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 329 4.8 %RANDOM
Rwork0.185 ---
obs0.185 6899 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.4207 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.35 Å20 Å20 Å2
2--8.35 Å20 Å2
3----16.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.14→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 7 33 1023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.14→2.27 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 61 5.4 %
Rwork0.256 1076 -
obs-1076 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3mli_msd.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_TOPOLOGY_INFILE_5

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