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- PDB-2vod: Crystal structure of N-terminal domains of Human La protein compl... -

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Basic information

Entry
Database: PDB / ID: 2vod
TitleCrystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUAUUUU
Components
  • 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'
  • LUPUS LA PROTEIN
KeywordsRNA BINDING PROTEIN / RNA RECOGNITION MOTIF / SYSTEMIC LUPUS ERYTHEMATOSUS / PHOSPHOPROTEIN / RNA MATURATION / RNA-BINDING PROTEIN / NUCLEUS / LA MOTIF / RNA-BINDING / POLYMORPHISM
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKotik-Kogan, O. / Valentine, E.R. / Sanfelice, D. / Conte, M.R. / Curry, S.
CitationJournal: Structure / Year: 2008
Title: Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3' Ends by the Human La Protein.
Authors: Kotik-Kogan, O. / Valentine, E.R. / Sanfelice, D. / Conte, M.R. / Curry, S.
History
DepositionFeb 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LUPUS LA PROTEIN
B: LUPUS LA PROTEIN
C: 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'
D: 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)49,3484
Polymers49,3484
Non-polymers00
Water2,954164
1
A: LUPUS LA PROTEIN
C: 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6742
Polymers24,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4.6 kcal/mol
Surface area14740 Å2
MethodPQS
2
B: LUPUS LA PROTEIN
D: 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6742
Polymers24,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-2.3 kcal/mol
Surface area14290 Å2
MethodPQS
Unit cell
Length a, b, c (Å)140.029, 44.471, 91.285
Angle α, β, γ (deg.)90.00, 114.35, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.646, 0.0167, -0.7631), (-0.0124, -0.9999, -0.0114), (-0.7632, 0.0021, 0.6462)
Vector: -6.8592, -35.5105, 14.7169)

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Components

#1: Protein LUPUS LA PROTEIN / HUMAN LA PROTEIN / SJOEGREN SYNDROME TYPE B ANTIGEN / SS-B / LA RIBONUCLEOPROTEIN / LA AUTOANTIGEN


Mass: 22529.809 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 4-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05455
#2: RNA chain 5'-R(*AP*UP*AP*UP*UP*UP*UP)-3'


Mass: 2144.283 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.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES ARE FROM VECTOR (GS) REMAINING SEQUENCE CORRESPONDS TO RESIDUES 4-194

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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: 2.64 Å3/Da / Density % sol: 52.98 % / Description: NONE
Crystal growpH: 5 / Details: pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87026
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87026 Å / Relative weight: 1
ReflectionResolution: 2.1→43 Å / Num. obs: 28656 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASER1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1693840.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1396 4.9 %RANDOM
Rwork0.232 ---
obs0.232 28656 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9873 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.96 Å20 Å24.04 Å2
2---6.85 Å20 Å2
3---0.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 282 0 164 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it3.662
X-RAY DIFFRACTIONc_scangle_it4.722.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 250 5.3 %
Rwork0.27 4467 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO-12.SC.PARDNA-RNA-MULTI-ENDO-12.SC.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.ED-12.PARION.ED-12.TOP

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