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- PDB-9hcz: Crystal structure of human TRF1 TRFH domain in complex with compound 6 -

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Basic information

Entry
Database: PDB / ID: 9hcz
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 6
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-(3-fluorophenoxy)-N,N-dimethylacetamide / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 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)26,1208
Polymers25,5561
Non-polymers5647
Water2,756153
1
A: Telomeric repeat-binding factor 1
hetero molecules

A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,23916
Polymers51,1122
Non-polymers1,12714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4450 Å2
ΔGint-26 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.876, 51.876, 147.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 160 molecules

#2: Chemical ChemComp-TT3 / 2-(3-fluorophenoxy)-N,N-dimethylacetamide


Mass: 197.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12FNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.53 %
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, 50 mM CaCl2 and 35-45 % PEG 200, 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: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.55→51.88 Å / Num. obs: 30074 / % possible obs: 99.5 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Χ2: 0.86 / Net I/σ(I): 15.1 / Num. measured all: 344509
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 94.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 1.202 / Num. measured all: 5654 / Num. unique obs: 1369 / CC1/2: 0.773 / Rpim(I) all: 0.649 / Rrim(I) all: 1.373 / Χ2: 0.61 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→19.63 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.086 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 1526 5.09 %RANDOM
Rwork0.1985 ---
obs0.1994 29967 99.4 %-
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.5712 Å20 Å20 Å2
2---5.5712 Å20 Å2
3---11.1424 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 35 155 1775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011706HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.842296HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d629SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it1706HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion15.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion231SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies17HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1688SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.56 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3591 -5.5 %
Rwork0.3075 567 -
all0.3106 600 -
obs--91.05 %
Refinement TLS params.Method: refined / Origin x: 3.5971 Å / Origin y: 19.2847 Å / Origin z: 16.085 Å
111213212223313233
T-0.0273 Å2-0.0023 Å2-0.0236 Å2--0.0722 Å20.0056 Å2---0.0704 Å2
L1.3311 °20.1693 °2-0.6383 °2-0.584 °2-0.1936 °2--1.3789 °2
S0.0561 Å °-0.0031 Å °0.0084 Å °0.0275 Å °0.0146 Å °0.0496 Å °0.0316 Å °-0.0907 Å °-0.0707 Å °
Refinement TLS groupSelection details: {A|63 - 266}

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