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- PDB-6f8d: Crystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form) -

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Basic information

Entry
Database: PDB / ID: 6f8d
TitleCrystal structure of Human ARS2 residues 171-270 + 408-763 (P65 form)
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 / mRNA processing / protein-macromolecule adaptor activity / nuclear body ...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 / mRNA processing / 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 / MOLECULAR REPLACEMENT / Resolution: 3.48 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 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Serrate RNA effector molecule homolog
C: Serrate RNA effector molecule homolog
B: Serrate RNA effector molecule homolog
D: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)106,3944
Polymers106,3944
Non-polymers00
Water00
1
A: Serrate RNA effector molecule homolog
C: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)53,1972
Polymers53,1972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-37 kcal/mol
Surface area24210 Å2
MethodPISA
2
B: Serrate RNA effector molecule homolog
D: Serrate RNA effector molecule homolog


Theoretical massNumber of molelcules
Total (without water)53,1972
Polymers53,1972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-34 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.210, 105.210, 267.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A176 - 761
2010B176 - 761

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Components

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


Mass: 12027.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 271-407 were deleted.Residues 171-270 and 408-763 were co-expressed as separate pieces.
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.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 271-407 were deleted.Residues 171-270 and 408-763 were co-expressed as separate pieces.
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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to ...Details: Crystals of ARS2 were obtained at 4 C in 2 microlitre hanging drops with a 1:1 ratio of protein solution (6 mg/ml in 20 mM HEPES, 300 mM NaCl, 2 mM tris(2-carboxyethyl)phosphine pH 7.8) to crystallisation solution. The crystallisation solution was 1.2 M sodium dihydrogen phosphate, 0.8 M dipotassium hydrogen phosphate, 0.2 M lithium sulphate, 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: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.48→91.11 Å / Num. obs: 20970 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.12 % / CC1/2: 0.997 / Rsym value: 0.114 / Net I/σ(I): 8.71
Reflection shellResolution: 3.48→3.57 Å / Redundancy: 2.98 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.253 / Rsym value: 1.617 / % possible all: 86.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F7J

6f7j


Resolution: 3.48→91.11 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.897 / SU B: 44.876 / SU ML: 0.614 / Cross valid method: THROUGHOUT / ESU R Free: 0.592 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29224 922 4.4 %RANDOM
Rwork0.26415 ---
obs0.26537 20048 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 160.658 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å21.3 Å20 Å2
2--2.6 Å2-0 Å2
3----8.44 Å2
Refinement stepCycle: 1 / Resolution: 3.48→91.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 0 0 6504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196619
X-RAY DIFFRACTIONr_bond_other_d0.0010.026288
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9658903
X-RAY DIFFRACTIONr_angle_other_deg0.818314576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71823.588354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.475151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7021572
X-RAY DIFFRACTIONr_chiral_restr0.0530.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021376
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_it3.50916.2153118
X-RAY DIFFRACTIONr_mcbond_other3.50916.2153117
X-RAY DIFFRACTIONr_mcangle_it6.01124.3163880
X-RAY DIFFRACTIONr_mcangle_other6.01124.3173881
X-RAY DIFFRACTIONr_scbond_it2.90516.5183501
X-RAY DIFFRACTIONr_scbond_other2.90516.5183502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.30924.6475024
X-RAY DIFFRACTIONr_long_range_B_refined9.2387187
X-RAY DIFFRACTIONr_long_range_B_other9.2387187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24180 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.479→3.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.483 60 -
Rwork0.446 1301 -
obs--86.03 %

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