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- PDB-9hf8: Crystal structure of human TRF1 TRFH domain in complex with compound 4 -

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Basic information

Entry
Database: PDB / ID: 9hf8
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 4
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
N-Benzyl-2-methoxyacetamide / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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: To Be Published
Title: Discovery of first-in-class inhibitors of the TRF1-TIN2 protein-protein interaction by fragment screening
Authors: Casale, G. / Guettler, S.
History
DepositionNov 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,9845
Polymers25,5561
Non-polymers4284
Water75742
1
A: Telomeric repeat-binding factor 1
hetero molecules

A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,96710
Polymers51,1122
Non-polymers8558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area3740 Å2
ΔGint-21 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.301, 85.301, 91.552
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-T9Q / N-Benzyl-2-methoxyacetamide / 2-methoxy-~{N}-(phenylmethyl)ethanamide


Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2 / 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.: 42 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
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: 2.19→57.49 Å / Num. obs: 20300 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 0.86 / Net I/σ(I): 14 / Num. measured all: 199918
Reflection shellResolution: 2.19→2.26 Å / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 2.636 / Num. measured all: 16133 / Num. unique obs: 1729 / CC1/2: 0.789 / Rpim(I) all: 0.91 / Rrim(I) all: 2.791 / Χ2: 0.78 / 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: 2.19→21.86 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.169 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1016 5.02 %RANDOM
Rwork0.2279 ---
obs0.2292 20230 99.9 %-
Displacement parametersBiso mean: 82.61 Å2
Baniso -1Baniso -2Baniso -3
1--11.8121 Å20 Å20 Å2
2---11.8121 Å20 Å2
3---23.6241 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.19→21.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 27 42 1571
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071586HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.782124HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d560SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes267HARMONIC5
X-RAY DIFFRACTIONt_it1586HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion15.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion211SEMIHARMONIC5
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_contact1343SEMIHARMONIC4
LS refinement shellResolution: 2.19→2.21 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4834 -4.94 %
Rwork0.433 385 -
all0.4354 405 -
obs--99.52 %
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)
14.2344-1.3017-4.72846.00483.93513.81590.06910.1753-0.32580.0364-0.63960.98020.2937-1.02110.5705-0.4501-0.0381-0.0186-0.16690.0259-0.310222.9027-4.9087-14.883
24.082-2.60232.075814.4703-0.678431.79740.66830.41250.2562-0.5806-0.2661-0.9552-0.70050.6264-0.4022-0.40450.05110.0408-0.29350.0516-0.292133.566-3.3714-21.7919
34.39680.0101-4.27826.6247-0.93937.73680.06330.30040.07330.1130.15990.4322-0.018-0.4721-0.2232-0.3478-0.0194-0.049-0.2222-0.0071-0.428130.3789-14.759-17.137
417.04372.53218.76836.89488.49212.3229-0.0837-1.47511.74581.288-0.4404-1.5758-1.06732.1180.52410.0407-0.0796-0.00250.2534-0.1394-0.206148.2021-14.1735-22.1563
56.9558-3.7658-2.60144.43141.887511.0131-0.15690.0519-0.9087-0.0609-0.06650.69721.1721-0.9770.2234-0.0411-0.0213-0.0253-0.17140.011-0.34837.0015-24.2463-27.7451
615.0584-0.0037-6.6972.0876-2.035116.3649-0.1256-1.38-0.32620.56630.0571-0.7422-0.56481.06070.0684-0.14890.1637-0.0138-0.1746-0.0894-0.502353.1645-22.8973-29.9407
711.68086.6235-6.70895.2475-2.12046.6069-0.4276-0.18-1.9284-0.03820.3908-0.70322.31470.46410.03670.33140.02720.00880.0174-0.1208-0.011350.1889-30.7219-37.8387
812.702-8.2618-9.08688.82396.21826.59350.44671.1932-0.8452-1.0448-0.96590.931-0.2977-1.36570.5192-0.20220.0002-0.1829-0.0993-0.0795-0.467429.9685-18.949-33.4365
90.4990.2368-3.676923.2167-8.97155.7380.45870.4830.3164-2.35160.09742.55340.0614-1.4969-0.5561-0.3220.1074-0.24570.3815-0.1220.044512.66261.1115-24.2719
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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