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

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Basic information

Entry
Database: PDB / ID: 2von
TitleCrystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUAAUUU
Components
  • 5'-R(*AP*UP*AP*AP*UP*UP*UP)-3'
  • LUPUS LA PROTEIN
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / RNA RECOGNITION MOTIF / SYSTEMIC LUPUS ERYTHEMATOSUS / PHOSPHOPROTEIN / RNA MATURATION / 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 modification / tRNA export from nucleus / 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 modification / tRNA export from nucleus / 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 / cytoplasm / cytosol
Similarity search - Function
RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / 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 / La protein, xRRM domain / xRRM domain profile. / 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 19, 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
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,3944
Polymers49,3944
Non-polymers00
Water3,711206
1
A: LUPUS LA PROTEIN
C: 5'-R(*AP*UP*AP*AP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6972
Polymers24,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-3.9 kcal/mol
Surface area14540 Å2
MethodPQS
2
B: LUPUS LA PROTEIN
D: 5'-R(*AP*UP*AP*AP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6972
Polymers24,6972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-4.2 kcal/mol
Surface area14140 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: (-0.6489, 0.0117, -0.7608), (-0.0087, -0.9999, -0.008), (0.7609, 0.0014, 0.6489)
Vector: -6.9078, -35.6483, 14.6216)

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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*AP*UP*UP*UP)-3'


Mass: 2167.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.63 Å3/Da / Density % sol: 52.79 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M phosphate citrate (pH 5.0), 22% (v/w) PEG 8000, 0.01 M taurine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.62
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2007 / Details: SINGLE SILICON (111) MONOCHROMATOR
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.1→43 Å / Num. obs: 27637 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.1 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZH5

1zh5


Resolution: 2.1→43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1804074.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1352 4.5 %RANDOM
Rwork0.23 ---
obs0.23 30111 97.7 %-
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.72 Å20 Å22.47 Å2
2---4.92 Å20 Å2
3---0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 286 0 206 3520
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it4.052
X-RAY DIFFRACTIONc_scangle_it5.282.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 240 4.8 %
Rwork0.251 4793 -
obs--99 %
Xplor fileSerial no: 1 / Param file: ION.ED-12.PARAM / Topol file: ION.ED-12.TOP

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