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- PDB-9wvh: Crystal structure of TONSL UBL domain -

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Basic information

Entry
Database: PDB / ID: 9wvh
TitleCrystal structure of TONSL UBL domain
ComponentsTonsoku-like protein
KeywordsCHAPERONE / Oligomerization / DNA repair / TONSL / Sponastrime dysplasia
Function / homology
Function and homology information


histone reader activity / nuclear replication fork / replication fork processing / protein localization to chromatin / double-strand break repair via homologous recombination / site of double-strand break / histone binding / nuclear body / nucleoplasm / cytoplasm
Similarity search - Function
: / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...: / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Leucine-rich repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / Ankyrin repeat-containing domain superfamily / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Tonsoku-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKarmakar, A. / Roy, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2022/001895 India
CitationJournal: To Be Published
Title: Crystal structure of TONSL UBL domain
Authors: Karmakar, A. / Roy, S.
History
DepositionSep 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tonsoku-like protein
B: Tonsoku-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5653
Polymers19,5422
Non-polymers231
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-32 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.147, 112.147, 69.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Tonsoku-like protein / Inhibitor of kappa B-related protein / I-kappa-B-related protein / IkappaBR / NF-kappa-B inhibitor- ...Inhibitor of kappa B-related protein / I-kappa-B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2


Mass: 9770.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TONSL, IKBR, NFKBIL2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Escherichia coli / References: UniProt: Q96HA7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-bicine pH 8.5, 0.5% PEG monomethyl ether 5000, 0.8 M Potassium sodium tartrate tetrahydrate, 10 mM DTT
PH range: 8.0-8.5 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS DIAMOND MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Aug 19, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.956→32.9 Å / Num. obs: 15431 / % possible obs: 99.87 % / Redundancy: 15 % / Biso Wilson estimate: 33.29 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1174 / Rpim(I) all: 0.03132 / Rrim(I) all: 0.1215 / Net I/σ(I): 18.07
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.769 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 5068 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.484 / % possible all: 99.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0110refinement
PROTEUM PLUS4.4.3data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→32.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 7.305 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20884 813 5 %RANDOM
Rwork0.19384 ---
obs0.19461 15431 99.89 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.96→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 1 95 1378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0171313
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161242
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.7951798
X-RAY DIFFRACTIONr_angle_other_deg0.4161.5582846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635.301166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44910209
X-RAY DIFFRACTIONr_chiral_restr0.0590.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
X-RAY DIFFRACTIONr_mcbond_it1.562.605633
X-RAY DIFFRACTIONr_mcbond_other1.5592.604633
X-RAY DIFFRACTIONr_mcangle_it2.6744.652786
X-RAY DIFFRACTIONr_mcangle_other2.6754.655787
X-RAY DIFFRACTIONr_scbond_it2.0032.944680
X-RAY DIFFRACTIONr_scbond_other1.9992.938678
X-RAY DIFFRACTIONr_scangle_other3.3625.2651013
X-RAY DIFFRACTIONr_long_range_B_refined6.27527.951402
X-RAY DIFFRACTIONr_long_range_B_other6.16326.871377
LS refinement shellResolution: 1.96→2.007 Å
RfactorNum. reflection% reflection
Rfree0.302 59 -
Rwork0.317 1121 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3049-0.2589-1.24941.44980.98824.10780.0294-0.31440.04520.1428-0.09680.0034-0.10630.00440.06740.0447-0.0126-0.03110.0933-0.0140.04447.32431.02545.764
22.1084-0.6126-2.10812.24271.22915.30550.03870.10950.0717-0.3171-0.1189-0.1079-0.1649-0.25440.08020.05210.0098-0.00340.06110.02530.060515.75826.88424.854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A930 - 1011
2X-RAY DIFFRACTION2B931 - 1011

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