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- PDB-6rr9: DNA/RNA binding protein -

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Basic information

Entry
Database: PDB / ID: 6rr9
TitleDNA/RNA binding protein
ComponentsSchlafen family member 5
KeywordsDNA BINDING PROTEIN / Zinc-finger protein / RNA-binding
Function / homology
Function and homology information


cell differentiation / ATP binding / nucleus
Similarity search - Function
: / Schlafen, GTPase-like domain / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Schlafen family member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.432 Å
AuthorsHuber, E. / Lammens, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchSFB1054 Germany
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural and biochemical characterization of human Schlafen 5.
Authors: Felix J Metzner / Elisabeth Huber / Karl-Peter Hopfner / Katja Lammens /
Abstract: The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA ...The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA processing. Here, we present the cryo-EM structure of full-length human Schlafen 5 (SLFN5) and the high-resolution crystal structure of the highly conserved N-terminal core domain. We show that the core domain does not resemble an ATPase-like fold and neither binds nor hydrolyzes ATP. SLFN5 binds tRNA as well as single- and double-stranded DNA, suggesting a potential role in transcriptional regulation. Unlike rat Slfn13 or human SLFN11, human SLFN5 did not cleave tRNA. Based on the structure, we identified two residues in proximity to the zinc finger motif that decreased DNA binding when mutated. These results indicate that Schlafen proteins have divergent enzymatic functions and provide a structural platform for future biochemical and genetic studies.
History
DepositionMay 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Advisory / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Schlafen family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7088
Polymers39,0711
Non-polymers6387
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-56 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.060, 101.060, 114.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Schlafen family member 5


Mass: 39070.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLFN5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08AF3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH5.0, 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 3.4→19.78 Å / Num. obs: 17172 / % possible obs: 98 % / Redundancy: 8.8 % / Net I/σ(I): 12.2
Reflection shellResolution: 3.4→3.63 Å / Num. unique obs: 2557

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.432→19.777 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 25.61 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2588 921 10.07 %
Rwork0.205 --
obs0.2104 9145 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.432→19.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 32 0 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132559
X-RAY DIFFRACTIONf_angle_d1.4143458
X-RAY DIFFRACTIONf_dihedral_angle_d22.191952
X-RAY DIFFRACTIONf_chiral_restr0.078382
X-RAY DIFFRACTIONf_plane_restr0.008441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4317-3.61160.33461130.30481022X-RAY DIFFRACTION86
3.6116-3.83640.30541310.25081154X-RAY DIFFRACTION100
3.8364-4.13010.28471390.21961181X-RAY DIFFRACTION100
4.1301-4.54120.22171360.19191202X-RAY DIFFRACTION100
4.5412-5.18790.23411270.18071188X-RAY DIFFRACTION100
5.1879-6.49750.26511340.20261214X-RAY DIFFRACTION100
6.4975-19.77690.22961410.16961263X-RAY DIFFRACTION99

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