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- PDB-9lri: Crystal Structure of Thermus thermophilus KhpB/EloR complexed with RNA -

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Basic information

Entry
Database: PDB / ID: 9lri
TitleCrystal Structure of Thermus thermophilus KhpB/EloR complexed with RNA
Components
  • Probable DNA/RNA-binding protein (Jag-related protein)
  • RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA-binding protein / KH domain / R3H domain / Thermus thermophilus / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA-binding protein KhpB, R3H domain / Jag, KH domain / RNA-binding protein KhpB / Putative single-stranded nucleic acids-binding domain / R3H domain / R3H domain / R3H domain superfamily / R3H domain profile. / K homology domain-like, alpha/beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / RNA / Probable DNA/RNA-binding protein (Jag-related protein)
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFukui, K. / Murakawa, T. / Yano, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: KH-R3H domain cooperation in RNA recognition by the global RNA-binding protein KhpB.
Authors: Fukui, K. / Murakawa, T. / Baba, S. / Kumasaka, T. / Yano, T.
History
DepositionJan 31, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable DNA/RNA-binding protein (Jag-related protein)
C: RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')
A: Probable DNA/RNA-binding protein (Jag-related protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4184
Polymers45,0953
Non-polymers3231
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.261, 46.058, 56.885
Angle α, β, γ (deg.)97.340, 92.530, 112.693
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Probable DNA/RNA-binding protein (Jag-related protein) / KhpB/EloR


Mass: 21044.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHA0442 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q5SL51
#2: RNA chain RNA (5'-R(P*CP*CP*CP*CP*CP*CP*C)-3')


Mass: 3006.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH 7.5), 0.2M ammonium sulfate, 25% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→36.99 Å / Num. obs: 10994 / % possible obs: 97.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 62.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.031 / Rrim(I) all: 0.103 / Net I/σ(I): 30.1
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.2 / Num. unique obs: 599 / CC1/2: 0.902 / Rpim(I) all: 0.088 / Rrim(I) all: 0.231 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
Coot0.9.8.92model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→32.382 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.883 / SU B: 13.405 / SU ML: 0.286 / Cross valid method: FREE R-VALUE / ESU R Free: 0.382
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2653 492 5.306 %
Rwork0.2036 8781 -
all0.207 --
obs-9273 97.724 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.036 Å20.016 Å20.088 Å2
2--0.055 Å20.088 Å2
3----0.105 Å2
Refinement stepCycle: LAST / Resolution: 2.65→32.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 140 21 5 2467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122519
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162351
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.6863442
X-RAY DIFFRACTIONr_angle_other_deg0.3841.575380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6865303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.308531
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.02858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12910368
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6310101
X-RAY DIFFRACTIONr_chiral_restr0.0540.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
X-RAY DIFFRACTIONr_nbd_refined0.2280.2524
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22070
X-RAY DIFFRACTIONr_nbtor_refined0.180.21220
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.223
X-RAY DIFFRACTIONr_nbd_other0.20.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.28
X-RAY DIFFRACTIONr_mcbond_it3.2913.7331218
X-RAY DIFFRACTIONr_mcbond_other3.2893.7321217
X-RAY DIFFRACTIONr_mcangle_it5.0616.7011519
X-RAY DIFFRACTIONr_mcangle_other5.066.7011520
X-RAY DIFFRACTIONr_scbond_it4.1694.391301
X-RAY DIFFRACTIONr_scbond_other4.1674.391302
X-RAY DIFFRACTIONr_scangle_it6.3117.8981923
X-RAY DIFFRACTIONr_scangle_other6.3097.8971924
X-RAY DIFFRACTIONr_lrange_it8.76349.1139905
X-RAY DIFFRACTIONr_lrange_other8.76349.1129906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.65-2.7180.383410.2526870.2597420.9180.96798.11320.248
2.718-2.7920.333330.2285930.2336400.9430.9797.81250.221
2.792-2.8730.276330.2456410.2466920.9520.96897.39880.237
2.873-2.960.288370.2315880.2346350.9510.96798.42520.227
2.96-3.0570.317310.2425730.2466190.9470.96597.57670.242
3.057-3.1630.298330.2255610.2296060.9370.96898.01980.228
3.163-3.2810.326240.2165580.225920.9320.97198.31080.223
3.281-3.4140.272250.2094980.2125300.9580.97598.67920.216
3.414-3.5640.292360.1965150.2025620.9570.97898.04270.207
3.564-3.7350.33280.2064420.2144770.9480.97498.53250.221
3.735-3.9340.189270.1944650.1945060.9710.97797.23320.218
3.934-4.1690.263250.1834200.1884620.9650.97996.32040.205
4.169-4.4520.191260.1573900.164350.9760.98495.63220.181
4.452-4.8010.209230.1743520.1763910.9740.98295.90790.21
4.801-5.2480.229120.183680.1813880.9690.98297.93810.209
5.248-5.8480.345190.2053130.2133370.9390.97898.51630.23
5.848-6.7160.276130.2392820.2412960.9640.9799.66220.27
6.716-8.1380.188130.1922330.1922480.9860.97999.19360.223
8.138-11.1620.17480.1591930.162090.9890.98696.17220.184
11.162-32.3820.19250.231090.2281180.9930.97396.61020.275

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