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- PDB-9hlr: Crystal structure of human TRF1 TRFH domain in complex with compo... -

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Basic information

Entry
Database: PDB / ID: 9hlr
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 15
ComponentsTelomeric repeat-binding factor 1
KeywordsPROTEIN BINDING / Telomere / Shelterin / Inhibitor
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation / shelterin complex ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / ankyrin repeat binding / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / Telomere Extension By Telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / DNA Damage/Telomere Stress Induced Senescence / spindle / fibrillar center / microtubule binding / chromosome, telomeric region / nuclear body / response to xenobiotic stimulus / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
2-(difluoromethoxy)benzene-1-sulfonamide / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCasale, G. / Le Bihan, Y.-V. / van Montfort, R.L.M. / Guettler, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214311/Z/18/Z United Kingdom
CitationJournal: Sci Rep / Year: 2025
Title: Discovery of first-in-class inhibitors of the TRF1:TIN2 protein:protein interaction by fragment screening.
Authors: Casale, G. / Liu, M. / Le Bihan, Y.V. / Inian, O. / Stammers, E. / Caldwell, J. / van Montfort, R.L.M. / Collins, I. / Guettler, S.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0285
Polymers25,5561
Non-polymers4724
Water50428
1
A: Telomeric repeat-binding factor 1
hetero molecules

A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05510
Polymers51,1122
Non-polymers9438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area4120 Å2
ΔGint-18 kcal/mol
Surface area19460 Å2
Unit cell
Length a, b, c (Å)85.016, 85.016, 91.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Telomeric repeat-binding factor 1 / NIMA-interacting protein 2 / TTAGGG repeat-binding factor 1 / Telomeric protein Pin2/TRF1


Mass: 25556.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Plasmid: pET His6 MBP Asn10 TEV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P54274
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-LL0 / 2-(difluoromethoxy)benzene-1-sulfonamide


Mass: 223.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7F2NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 ...Details: 150 nanoliter of TRF1 TRFH at 28.6 mg/mL plus 150 nanoliter of a crystallisation solution consisting of 0.1 M MES pH 6, 1-12 mM Mg(OAc)2, 1% PEG8000, and 10-15% glycerol, against 35 microliter of crystallisation solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.48→57.39 Å / Num. obs: 13996 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Rrim(I) all: 0.106 / Χ2: 0.66 / Net I/σ(I): 8.5 / Num. measured all: 134485
Reflection shellResolution: 2.48→2.58 Å / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 1.643 / Num. measured all: 15613 / Num. unique obs: 1552 / CC1/2: 0.855 / Rpim(I) all: 0.543 / Rrim(I) all: 1.731 / Χ2: 0.4 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→57.39 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.277 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.229
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 952 6.83 %RANDOM
Rwork0.2347 ---
obs0.237 13948 99.8 %-
Displacement parametersBiso mean: 101.15 Å2
Baniso -1Baniso -2Baniso -3
1--17.5563 Å20 Å20 Å2
2---17.5563 Å20 Å2
3---35.1126 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.48→57.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 28 28 1622
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071660HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.862236HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d587SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes281HARMONIC5
X-RAY DIFFRACTIONt_it1660HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.25
X-RAY DIFFRACTIONt_other_torsion17.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion222SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1407SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.5 Å / Total num. of bins used: 48
RfactorNum. reflection% reflection
Rfree0.3373 -6.06 %
Rwork0.3814 279 -
all0.3788 297 -
obs--100 %
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)
17.0849-0.4197-4.66286.08690.903700.3155-0.0341-0.5021-0.2947-1.0581.0496-0.638-0.74610.7426-0.7753-0.0505-0.016-0.560.0114-0.619622.6137-4.986130.8078
29.8361-6.1024-4.892120.63185.74245.39630.89010.54580.49-0.7502-0.9421-1.6169-1.85921.18520.052-0.86910.00950.0258-0.76780.0492-0.575833.3166-3.459723.8937
310.0263-2.4144-11.23177.69751.662123.6694-0.11840.6572-0.23860.01750.19080.46340.1757-1.0425-0.0725-0.7737-0.0245-0.0226-0.6907-0.0059-0.716330.2921-14.756728.3733
46.35422.994310.754313.12461.733224.2566-0.3646-1.50792.87892.0299-0.8381-1.6589-2.96171.69041.20270.6027-0.0466-0.01110.7751-0.14830.410947.6746-14.587822.8959
56.9504-2.8319-3.33533.35511.138411.0881-0.0253-0.0631-0.88280.1395-0.11190.39991.064-0.62190.1372-0.4087-0.0495-0.0143-0.5776-0.0002-0.668636.5306-24.283617.5254
627.62139.7931-6.90242.1010.020312.6852-0.3217-1.7519-1.12410.6830.4537-1.09420.29910.9532-0.132-0.36240.2650.0688-0.3879-0.0745-0.672652.3734-23.66315.4472
719.31624.0313-3.710816.2228-0.801821.1804-0.5769-0.0913-1.94920.14970.0793-0.09282.8403-0.87570.49760.0120.0790.064-0.1925-0.1154-0.307549.4923-30.33447.1982
821.2816-10.3845-9.633611.93856.84548.07710.58431.3608-0.8361-0.9272-1.39421.2124-0.4713-2.0030.8099-0.53790.0257-0.1811-0.3766-0.0906-0.692730.2498-18.99611.5281
9-0.2114-1.7947-5.72046.8511-0.210600.96710.20131.2898-2.4771-0.43622.1504-0.6466-1.5944-0.5309-0.93090.2199-0.2351-0.2667-0.174-0.376612.5720.796621.8405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|62 - 92}
2X-RAY DIFFRACTION2{A|93 - 111}
3X-RAY DIFFRACTION3{A|112 - 134}
4X-RAY DIFFRACTION4{A|135 - 149}
5X-RAY DIFFRACTION5{A|150 - 186}
6X-RAY DIFFRACTION6{A|187 - 200}
7X-RAY DIFFRACTION7{A|201 - 225}
8X-RAY DIFFRACTION8{A|226 - 253}
9X-RAY DIFFRACTION9{A|254 - 268}

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