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

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Basic information

Entry
Database: PDB / ID: 9hda
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 58
ComponentsTelomeric repeat-binding factor 1
KeywordsPROTEIN BINDING / Telomere / Inhibitor / Shelterin
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
4-IODOPYRAZOLE / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 12, 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)26,1306
Polymers25,5561
Non-polymers5745
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)52,26012
Polymers51,1122
Non-polymers1,14810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4860 Å2
ΔGint-13 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.272, 52.272, 146.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3IN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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: 1.95 Å3/Da / Density % sol: 36.98 %
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: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 2.1→52.27 Å / Num. obs: 12580 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.03 / Rrim(I) all: 0.11 / Χ2: 0.97 / Net I/σ(I): 13.9 / Num. measured all: 178320
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 2.796 / Num. measured all: 14549 / Num. unique obs: 989 / CC1/2: 0.81 / Rpim(I) all: 0.761 / Rrim(I) all: 2.899 / Χ2: 0.85 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.22 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.262 / SU Rfree Blow DPI: 0.215 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 649 5.18 %RANDOM
Rwork0.2317 ---
obs0.2343 12518 100 %-
Displacement parametersBiso mean: 69.47 Å2
Baniso -1Baniso -2Baniso -3
1--11.6944 Å20 Å20 Å2
2---11.6944 Å20 Å2
3---23.3888 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 24 42 1589
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081581HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.792131HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d535SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes274HARMONIC5
X-RAY DIFFRACTIONt_it1581HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion17.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion220SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1237SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.12 Å / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.2684 -4.85 %
Rwork0.3527 373 -
all0.3485 392 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.4854 Å / Origin y: 6.3578 Å / Origin z: 16.1212 Å
111213212223313233
T-0.3704 Å2-0.0367 Å20.0728 Å2--0.6736 Å2-0.0316 Å2---0.4519 Å2
L2.9987 °2-0.683 °21.8388 °2-0.4866 °2-0.3518 °2--3.8488 °2
S-0.0598 Å °-0.0424 Å °-0.0735 Å °0.2008 Å °0.0817 Å °0.0273 Å °0.229 Å °0.1576 Å °-0.0219 Å °
Refinement TLS groupSelection details: {A|63 - 266}

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