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- PDB-1yty: Structural basis for recognition of UUUOH 3'-terminii of nascent ... -

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Basic information

Entry
Database: PDB / ID: 1yty
TitleStructural basis for recognition of UUUOH 3'-terminii of nascent RNA pol III transcripts by La autoantigen
Components
  • 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
  • Lupus La protein
KeywordsTRANSCRIPTION/RNA / Protein-RNA complex / TRANSCRIPTION-RNA COMPLEX
Function / homology
Function and homology information


nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / tRNA export from nucleus / tRNA modification / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal ...nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / tRNA export from nucleus / tRNA modification / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / sequence-specific mRNA binding / poly(U) RNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 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 / Lupus La protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsTeplova, M. / Yuan, Y.R. / Ilin, S. / Malinina, L. / Phan, A.T. / Teplov, A. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Basis for Recognition and Sequestration of UUU(OH) 3' Temini of Nascent RNA Polymerase III Transcripts by La, a Rheumatic Disease Autoantigen.
Authors: Teplova, M. / Yuan, Y.R. / Phan, A.T. / Malinina, L. / Ilin, S. / Teplov, A. / Patel, D.J.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
D: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
A: Lupus La protein
B: Lupus La protein


Theoretical massNumber of molelcules
Total (without water)51,4784
Polymers51,4784
Non-polymers00
Water2,324129
1
C: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
A: Lupus La protein


Theoretical massNumber of molelcules
Total (without water)25,7392
Polymers25,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'
B: Lupus La protein


Theoretical massNumber of molelcules
Total (without water)25,7392
Polymers25,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.690, 54.001, 56.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ASN / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 7 - 189 / Label seq-ID: 7 - 189

Dom-IDAuth asym-IDLabel asym-ID
1AC
2BD
DetailsMonomer. There are two copies at one asymmetric unit related by NCS 2-fold axis

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Components

#1: RNA chain 5'-R(*UP*GP*CP*UP*GP*UP*UP*UP*U)-3'


Mass: 2787.631 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Lupus La protein / Sjogren syndrome type B antigen / SS-B / La ribonucleoprotein / La autoantigen


Mass: 22951.543 Da / Num. of mol.: 2 / Fragment: residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSB / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P05455
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 3350, lithium sulfate, potassium chloride, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2lithium sulfate11
3potassium chloride11
4acetate11
5H2O11
6PEG 335012
7lithium sulfate12
8potassium chloride12
9acetate12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97946 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 20734 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.148 / Rsym value: 0.148
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.451 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.859 / SU B: 15.38 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.374 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28829 1114 5.1 %RANDOM
Rwork0.21866 ---
obs0.22213 20734 99.51 %-
all-20734 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.661 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2---1.03 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.29→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 366 0 129 3533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223502
X-RAY DIFFRACTIONr_angle_refined_deg1.7262.1094787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2035365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97224.967151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74815617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1761516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022462
X-RAY DIFFRACTIONr_nbd_refined0.210.21361
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.215
X-RAY DIFFRACTIONr_mcbond_it0.9291.51910
X-RAY DIFFRACTIONr_mcangle_it1.47122986
X-RAY DIFFRACTIONr_scbond_it2.32831898
X-RAY DIFFRACTIONr_scangle_it3.5714.51801
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1515 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.370.5
medium thermal0.942
LS refinement shellResolution: 2.292→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 92 -
Rwork0.217 1413 -
obs--93.71 %
Refinement TLS params.Method: refined / Origin x: 39.9977 Å / Origin y: -2.3111 Å / Origin z: -42.4449 Å
111213212223313233
T-0.0332 Å2-0.0188 Å2-0.0015 Å2--0.0971 Å20.0036 Å2---0.1334 Å2
L1.1668 °2-0.6687 °20.0428 °2-0.8005 °2-0.0535 °2--0.3996 °2
S-0.0033 Å °0.0661 Å °-0.0691 Å °-0.0513 Å °0.0076 Å °0.0295 Å °0.011 Å °0.0043 Å °-0.0043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC6 - 1886 - 188
2X-RAY DIFFRACTION1BD7 - 1887 - 188
3X-RAY DIFFRACTION1CA1 - 91 - 9
4X-RAY DIFFRACTION1DB1 - 91 - 9

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