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

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Basic information

Entry
Database: PDB / ID: 2voo
TitleCrystal structure of N-terminal domains of Human La protein complexed with RNA oligomer UUUUUUUU
Components
  • 5'-R(*UP*UP*UP*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: 1.8 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: LUPUS LA PROTEIN
C: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'
D: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)49,2564
Polymers49,2564
Non-polymers00
Water3,621201
1
A: LUPUS LA PROTEIN
C: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6282
Polymers24,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-3.6 kcal/mol
Surface area12940 Å2
MethodPQS
2
B: LUPUS LA PROTEIN
D: 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3'


Theoretical massNumber of molelcules
Total (without water)24,6282
Polymers24,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-2.7 kcal/mol
Surface area12810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)98.309, 114.586, 37.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9966, -0.0782, -0.0249), (0.0782, -0.9969, 0.0039), (0.0251, -0.002, -0.9997)
Vector: -0.4831, -57.3223, -19.5949)

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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(*UP*UP*UP*UP*UP*UP*UP)-3'


Mass: 2098.203 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.: 201 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST TWO RESIDUES ARE FROM VECTOR (GS) REMAINS, 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: 2.33 Å3/Da / Density % sol: 46.81 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.62
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 13, 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: 2.1→41 Å / Num. obs: 3 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 1.8 / % possible all: 97.7

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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: 1.8→37.31 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1715061.49 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1979 5 %RANDOM
Rwork0.25 ---
obs0.25 39488 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0525 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å20 Å20 Å2
2---0.19 Å20 Å2
3---4.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 114 0 201 3229
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_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it3.212
X-RAY DIFFRACTIONc_scangle_it4.32.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 336 5.3 %
Rwork0.293 6063 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ION.ED-12.PARAMION.ED-12.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-END-12.SC.PARAMDNA-RNA-MULTI-ENDO-12.SC.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4DNA-RNA-MULTI-END-12.SC.PARAMION.ED-12.TOP

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