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- PDB-7q3z: DNA/RNA binding protein -

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Basic information

Entry
Database: PDB / ID: 7q3z
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
DepositionOct 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Schlafen family member 5
A: Schlafen family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8346
Polymers77,6572
Non-polymers1774
Water5,224290
1
B: Schlafen family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9173
Polymers38,8281
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Schlafen family member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9173
Polymers38,8281
Non-polymers882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.880, 64.040, 104.580
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Schlafen family member 5


Mass: 38828.363 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 200 mM NaCl, 100 mM MES pH 5.8, 20% (v/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45.9 Å / Num. obs: 108773 / % possible obs: 98.8 % / Redundancy: 10.2 % / Rrim(I) all: 0.086 / Net I/σ(I): 12.86
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 7909 / Rrim(I) all: 1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RR9

6rr9


Resolution: 1.85→45.9 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 2695 4.84 %
Rwork0.1875 --
obs0.1888 55695 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 4 290 5162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075091
X-RAY DIFFRACTIONf_angle_d0.8546901
X-RAY DIFFRACTIONf_dihedral_angle_d15.831934
X-RAY DIFFRACTIONf_chiral_restr0.057770
X-RAY DIFFRACTIONf_plane_restr0.006889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.34241330.31982746X-RAY DIFFRACTION98
1.88-1.920.34431510.30962736X-RAY DIFFRACTION98
1.92-1.960.33471220.2732702X-RAY DIFFRACTION98
1.96-20.26551420.23892813X-RAY DIFFRACTION98
2-2.050.32941230.2242746X-RAY DIFFRACTION98
2.05-2.10.25791300.21492776X-RAY DIFFRACTION98
2.1-2.160.23931190.21382785X-RAY DIFFRACTION99
2.16-2.220.24321260.20142796X-RAY DIFFRACTION99
2.22-2.290.24161320.19692798X-RAY DIFFRACTION99
2.29-2.370.24451460.19552810X-RAY DIFFRACTION99
2.37-2.470.24771160.19812796X-RAY DIFFRACTION99
2.47-2.580.18371450.18812787X-RAY DIFFRACTION99
2.58-2.720.26271590.19252786X-RAY DIFFRACTION99
2.72-2.890.22411470.18652798X-RAY DIFFRACTION99
2.89-3.110.26351570.19552815X-RAY DIFFRACTION99
3.11-3.420.22581490.17582797X-RAY DIFFRACTION100
3.42-3.920.18761540.16412816X-RAY DIFFRACTION100
3.92-4.930.1521510.14792856X-RAY DIFFRACTION100
4.94-45.90.17871930.18322841X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 31.4167 Å / Origin y: -15.3696 Å / Origin z: 82.2544 Å
111213212223313233
T0.1831 Å2-0.0136 Å2-0.0074 Å2-0.2418 Å20.0007 Å2--0.2081 Å2
L0.2776 °2-0.0286 °2-0.114 °2-0.0613 °20.1216 °2--0.5966 °2
S-0.0005 Å °0.1466 Å °-0.0067 Å °-0.0262 Å °-0.0073 Å °0.017 Å °0.0526 Å °-0.0812 Å °0.0062 Å °
Refinement TLS groupSelection details: all

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