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

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Basic information

Entry
Database: PDB / ID: 9hlp
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 18
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
: / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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)26,1617
Polymers25,5561
Non-polymers6056
Water1,08160
1
A: Telomeric repeat-binding factor 1
hetero molecules

A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,32214
Polymers51,1122
Non-polymers1,21012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5120 Å2
ΔGint-8 kcal/mol
Surface area19310 Å2
Unit cell
Length a, b, c (Å)85.198, 85.198, 91.102
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-A1IV7 / 1-piperidin-4-ylindole


Mass: 200.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.73 Å3/Da / Density % sol: 67.07 %
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: 2.24→57.34 Å / Num. obs: 18844 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Χ2: 0.92 / Net I/σ(I): 14.7 / Num. measured all: 186023
Reflection shellResolution: 2.24→2.31 Å / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 2.592 / Num. measured all: 17186 / Num. unique obs: 1703 / CC1/2: 0.858 / Rpim(I) all: 0.853 / Rrim(I) all: 2.73 / Χ2: 0.87 / Net I/σ(I) obs: 0.9

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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: 2.24→57.34 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 1045 5.55 %RANDOM
Rwork0.2356 ---
obs0.2367 18815 100 %-
Displacement parametersBiso mean: 91.2 Å2
Baniso -1Baniso -2Baniso -3
1--15.5852 Å20 Å20 Å2
2---15.5852 Å20 Å2
3---31.1703 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.24→57.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1501 0 37 60 1598
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071604HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822157HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d570SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes275HARMONIC5
X-RAY DIFFRACTIONt_it1604HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion16.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion215SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1337SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.26 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5622 -3.71 %
Rwork0.4304 363 -
all0.434 377 -
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)
11.3609-0.3282-0.27374.06821.13810.3640.20410.1133-0.00340.0103-0.09410.13660.1736-0.1756-0.11-0.9739-0.0296-0.0148-0.72620.047-0.921228.1741-7.7062-17.4594
29.9009-2.85531.871519.7643-29.16539.88420.2123-1.62173.48512.4928-0.8399-1.4332-2.79982.76040.62760.18750.0710.11690.62950.02580.081746.6228-15.8054-25.1098
37.4346-1.7045-0.63453.11771.17126.2505-0.042-0.1051-0.75030.0641-0.04110.46321.1966-0.49390.0831-0.7007-0.0825-0.0077-0.81820.0156-0.942137.242-23.9687-27.9432
46.3423.3838-8.24841.7933-1.44740.00330.0263-0.7859-0.40290.1236-0.1074-0.6722-0.04641.29370.0811-0.87170.117-0.0381-0.7461-0.0054-1.07452.9734-23.5947-29.445
511.592110.277-2.562725.1859-3.163623.95570.1667-1.0995-2.0277-0.0775-0.30531.30973.7551-0.47110.13860.65930.2774-0.07790.114-0.09990.163949.6005-33.1381-35.1804
612.2414-5.7972-6.91334.58194.48747.43180.31090.9182-0.2417-0.8288-0.61970.56450.0424-1.10970.3088-0.769-0.0414-0.1235-0.8555-0.0208-1.037533.508-19.9878-35.0291
7-3.08994.077-11.750126.0011-9.48443.69640.90651.51541.4102-4.08030.47462.6189-1.001-2.0261-1.3811-0.26350.029-0.21830.4656-0.10570.276712.72431.0423-24.2277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|62 - 134}
2X-RAY DIFFRACTION2{A|135 - 149}
3X-RAY DIFFRACTION3{A|150 - 187}
4X-RAY DIFFRACTION4{A|188 - 200}
5X-RAY DIFFRACTION5{A|201 - 219}
6X-RAY DIFFRACTION6{A|220 - 253}
7X-RAY DIFFRACTION7{A|254 - 268}

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