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- PDB-9kop: Crystal structure of the Trove domain -

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Basic information

Entry
Database: PDB / ID: 9kop
TitleCrystal structure of the Trove domain
ComponentsTROVE domain-containing protein
KeywordsRNA BINDING PROTEIN / trove / ro60 / phage
Function / homologyTROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain profile. / von Willebrand factor A-like domain superfamily / ribonucleoprotein complex / RNA binding / metal ion binding / TROVE domain-containing protein
Function and homology information
Biological speciesThermus phage phiLo (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHu, Z. / Huang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and molecular mechanisms of an Ro60 homolog from a Thermus bacteriophage.
Authors: Zetao Hu / Zhaohui Jin / Lulu Guo / Ling Zeng / Xuanjia Dong / Lin Jiang / Wenting Dai / Jinbiao Ma / Ying Huang /
Abstract: Ro60 is a conserved RNA-binding protein essential for RNA quality control and implicated in autoimmune responses. In this study, we present the structural and functional characterization of φRo60, ...Ro60 is a conserved RNA-binding protein essential for RNA quality control and implicated in autoimmune responses. In this study, we present the structural and functional characterization of φRo60, an Ro60 homolog from Thermus phage phiLo, with its crystal structure determined at 1.99 Å. Despite limited sequence identity with bacterial and amphibian homologs, φRo60 maintains the canonical doughnut-shaped architecture comprising HEAT repeats and a von Willebrand factor A domain. Surface electrostatic analysis reveals an extensive positively charged region across multiple α-helices, likely facilitating diverse RNA interactions. Moreover, φRo60 binds two Y RNA-like molecules (Yrl1 and Yrl2), identified from the phiLo genome, with distinct stoichiometries, leading to the formation of higher-order nucleocytoplasmic ribonucleoprotein (RNP) complexes. Cryo-electron microscopy of φRo60-Yrl2 RNP complexes revealed a minor population adopting a dimeric assembly, and key positively charged residues are important for φRo60-Yrl2 interactions. Additionally, φRo60 and Yrls interact with host Thermus thermophilus HB8 polynucleotide phosphorylase (PNPase), forming tripartite RYPER-like complexes and attenuating the ribonuclease activity of PNPase. These findings highlight φRo60 as a structurally adaptable Ro60 homolog capable of diverse RNA interactions and host factor recruitment, implying unique strategies for phages to counteract host defense systems in thermophilic environments.
History
DepositionNov 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROVE domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2102
Polymers57,1701
Non-polymers401
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.877, 60.124, 65.590
Angle α, β, γ (deg.)90.000, 100.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TROVE domain-containing protein


Mass: 57169.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage phiLo (virus) / Gene: phiLo_26 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S7URH6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 0.1 M MES,pH 6.0, 6% Tacsimate,pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.99→64.47 Å / Num. obs: 33397 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 25.72 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4818

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→49.79 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 1993 5.97 %
Rwork0.1737 31369 -
obs0.1753 33362 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 1.99→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 1 301 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923777
X-RAY DIFFRACTIONf_angle_d1.07915117
X-RAY DIFFRACTIONf_chiral_restr0.0605569
X-RAY DIFFRACTIONf_plane_restr0.011650
X-RAY DIFFRACTIONf_dihedral_angle_d5.389513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.24341410.21752210X-RAY DIFFRACTION99.92
2.04-2.10.251450.20332207X-RAY DIFFRACTION99.87
2.1-2.160.26251440.19422230X-RAY DIFFRACTION99.96
2.16-2.230.19641380.18132271X-RAY DIFFRACTION99.79
2.23-2.310.23531440.17532220X-RAY DIFFRACTION99.96
2.31-2.40.22261410.18032233X-RAY DIFFRACTION99.87
2.4-2.510.24071420.1752247X-RAY DIFFRACTION99.92
2.51-2.650.2511440.17812229X-RAY DIFFRACTION99.96
2.65-2.810.21021450.17522222X-RAY DIFFRACTION99.87
2.81-3.030.20231410.17872264X-RAY DIFFRACTION99.92
3.03-3.330.18381410.17382236X-RAY DIFFRACTION99.71
3.33-3.820.1841420.162249X-RAY DIFFRACTION99.17
3.82-4.810.15931410.14872240X-RAY DIFFRACTION99.04
4.81-49.790.17871440.18362311X-RAY DIFFRACTION98.87
Refinement TLS params.Method: refined / Origin x: -3.01934840221 Å / Origin y: 11.4987476931 Å / Origin z: 17.3277668202 Å
111213212223313233
T0.0688851742219 Å2-0.0139142901505 Å2-0.00482253349103 Å2-0.0808478659619 Å20.00992028107034 Å2--0.0658976964623 Å2
L-0.0375771274747 °2-0.0935541841705 °2-0.0612287036822 °2-0.509868015075 °2-0.00598751483485 °2--0.150189116279 °2
S0.0163391972728 Å °0.00896612157062 Å °-0.00476126519729 Å °-0.0713080059232 Å °-0.024766978319 Å °-0.00529269620598 Å °-0.00173005817181 Å °-0.014495394722 Å °1.08448286472E-10 Å °
Refinement TLS groupSelection details: all

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