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

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Basic information

Entry
Database: PDB / ID: 2vop
TitleCrystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUUUU
Components
  • 5'-R(*AP*UP*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: 2.8 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,2314
Polymers24,0392
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-4.3 kcal/mol
Surface area13300 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.070, 116.690, 63.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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.: 1 / 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*UP*UP*UP)-3'


Mass: 1508.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
Sequence detailsFIRST TWO RESIDUES ARE FROM VECTOR (GS) REMAINING SEQUENCE CORRESPONDS 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: 4.15 Å3/Da / Density % sol: 70.16 % / Description: NONE

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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: Jul 12, 2006 / 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: 2.8→63 Å / Num. obs: 8894 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 76.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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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: 2.8→48.24 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1603544.48 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 494 5.6 %RANDOM
Rwork0.261 ---
obs0.261 8894 97.5 %-
Displacement parametersBiso mean: 56.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 99 10 0 1540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 2.8→2.98 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.401 --
Rwork0.362 1384 -
obs--99.7 %

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