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- PDB-6f7j: Crystal structure of Human ARS2 residues 171-270 + 408-763 -

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Basic information

Entry
Database: PDB / ID: 6f7j
TitleCrystal structure of Human ARS2 residues 171-270 + 408-763
Components(Serrate RNA effector molecule homolog) x 2
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / protein-macromolecule adaptor activity / nuclear body / ribonucleoprotein complex ...mRNA cap binding complex binding / neuronal stem cell population maintenance / primary miRNA processing / response to arsenic-containing substance / positive regulation of neurogenesis / RNA polymerase II transcribes snRNA genes / mRNA Splicing - Major Pathway / protein-macromolecule adaptor activity / nuclear body / ribonucleoprotein complex / regulation of DNA-templated transcription / protein-containing complex / DNA binding / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / RNA-binding domain superfamily
Similarity search - Domain/homology
Serrate RNA effector molecule homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.22 Å
AuthorsCusack, S. / Schulze, W.M.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council322586 France
CitationJournal: Nat Commun / Year: 2018
Title: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.
Authors: Schulze, W.M. / Stein, F. / Rettel, M. / Nanao, M. / Cusack, S.
History
DepositionDec 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Serrate RNA effector molecule homolog
B: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)53,1972
Polymers53,1972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-41 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.920, 90.920, 267.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Serrate RNA effector molecule homolog / Arsenite-resistance protein 2


Mass: 12027.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 171-270 and 408-763 were co-expressed.Residues 271-407 were deleted
Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5
#2: Protein Serrate RNA effector molecule homolog / Arsenite-resistance protein 2


Mass: 41169.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 171-270 and 408-763 were co-expressed.Residues 271-407 were deleted
Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: Q9BXP5

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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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: Protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8, mixed 1:1 with reservoir solution containing 1.2 M sodium dihydrogen phosphate, 0.8 M ...Details: Protein solution at 6 mg per ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8, mixed 1:1 with reservoir solution containing 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate and 0.1 M CAPS pH 10.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.22→78.74 Å / Num. obs: 10951 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.13 % / CC1/2: 0.996 / Rsym value: 0.259 / Net I/σ(I): 10.15
Reflection shellResolution: 3.22→3.3 Å / Redundancy: 9.13 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 805 / CC1/2: 0.544 / Rsym value: 1.67 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.22→78.74 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.779 / SU B: 33.469 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32174 516 4.7 %RANDOM
Rwork0.28867 ---
obs0.29033 10435 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----1.66 Å2
Refinement stepCycle: 1 / Resolution: 3.22→78.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 0 0 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193508
X-RAY DIFFRACTIONr_bond_other_d0.0010.023334
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9674719
X-RAY DIFFRACTIONr_angle_other_deg0.81437737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92723.73185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.391536
X-RAY DIFFRACTIONr_chiral_restr0.0520.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9758.2921656
X-RAY DIFFRACTIONr_mcbond_other0.9758.2921655
X-RAY DIFFRACTIONr_mcangle_it1.78212.4382063
X-RAY DIFFRACTIONr_mcangle_other1.78212.4382064
X-RAY DIFFRACTIONr_scbond_it0.7168.3721852
X-RAY DIFFRACTIONr_scbond_other0.7158.3721853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.36512.5072657
X-RAY DIFFRACTIONr_long_range_B_refined2.99593.8083781
X-RAY DIFFRACTIONr_long_range_B_other2.99593.83781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.223→3.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 32 -
Rwork0.39 773 -
obs--99.38 %

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