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- PDB-4wkr: LaRP7 wrapping up the 3' hairpin of 7SK non-coding RNA (302-332) -

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Basic information

Entry
Database: PDB / ID: 4wkr
TitleLaRP7 wrapping up the 3' hairpin of 7SK non-coding RNA (302-332)
Components
  • 7SK GGHP4 (300-332)
  • La-related protein 7
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / RNA RECOGNITION MOTIF / PHOSPHOPROTEIN / PROTEIN / NUCLEUS / LA MOTIF
Function / homology
Function and homology information


U6 2'-O-snRNA methylation / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body / : / negative regulation of viral transcription / regulation of mRNA splicing, via spliceosome / negative regulation of transcription elongation by RNA polymerase II ...U6 2'-O-snRNA methylation / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of protein localization to Cajal body / : / negative regulation of viral transcription / regulation of mRNA splicing, via spliceosome / negative regulation of transcription elongation by RNA polymerase II / U6 snRNA binding / RNA splicing / mRNA processing / spermatogenesis / cell differentiation / ribonucleoprotein complex / mRNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function ...LARP7, RNA recognition motif 1 / LARP7, RNA recognition motif 2 / La-related protein 7, La domain / RNA binding motif / Lupus La protein / xRRM domain profile. / La protein, xRRM domain / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / La-related protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsUchikawa, E. / Natchiar, K.S. / Han, X. / Proux, F. / Roblin, P. / Zhang, E. / Durand, A. / Klaholz, B.P. / Dock-Bregeon, A.-C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7.
Authors: Uchikawa, E. / Natchiar, K.S. / Han, X. / Proux, F. / Roblin, P. / Zhang, E. / Durand, A. / Klaholz, B.P. / Dock-Bregeon, A.C.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Jan 10, 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: La-related protein 7
B: La-related protein 7
C: 7SK GGHP4 (300-332)
D: 7SK GGHP4 (300-332)


Theoretical massNumber of molelcules
Total (without water)67,7174
Polymers67,7174
Non-polymers00
Water905
1
A: La-related protein 7
C: 7SK GGHP4 (300-332)


Theoretical massNumber of molelcules
Total (without water)33,8582
Polymers33,8582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: La-related protein 7
D: 7SK GGHP4 (300-332)


Theoretical massNumber of molelcules
Total (without water)33,8582
Polymers33,8582
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.452, 33.500, 119.080
Angle α, β, γ (deg.)90.00, 128.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein La-related protein 7 / La ribonucleoprotein domain family member 7 / P-TEFb-interaction protein for 7SK stability / PIP7S


Mass: 24022.566 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, UNP Residues 1-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP7, HDCMA18P / Plasmid: PET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: Q4G0J3
#2: RNA chain 7SK GGHP4 (300-332)


Mass: 9835.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG 3350 & 0.1 M succinic acid, pH 7.0 / PH range: 7

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→92.58 Å / Num. all: 27542 / Num. obs: 8165 / % possible obs: 95.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 106.93 Å2 / Net I/σ(I): 5.41
Reflection shellResolution: 3.2→3.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / % possible all: 94.9

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VOO

2voo


Resolution: 3.2→59.06 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.9051 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.505
RfactorNum. reflection% reflectionSelection details
Rfree0.274 382 4.68 %RANDOM
Rwork0.2206 ---
obs0.2232 8155 94.04 %-
Displacement parametersBiso mean: 93.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.9841 Å20 Å2-14.7608 Å2
2--6.3558 Å20 Å2
3---1.6283 Å2
Refine analyzeLuzzati coordinate error obs: 0.707 Å
Refinement stepCycle: 1 / Resolution: 3.2→59.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 168 0 5 2695
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012749HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.323743HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d990SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes386HARMONIC5
X-RAY DIFFRACTIONt_it2749HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion24.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3109SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.58 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3076 111 4.92 %
Rwork0.257 2146 -
all0.2596 2257 -
obs--94.04 %

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