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- PDB-9hd2: Crystal structure of human TRF1 TRFH domain in complex with compo... -

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Basic information

Entry
Database: PDB / ID: 9hd2
TitleCrystal structure of human TRF1 TRFH domain in complex with compound 40
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 / molecular replacement / Resolution: 2.07 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1736
Polymers25,5561
Non-polymers6175
Water86548
1
A: Telomeric repeat-binding factor 1
hetero molecules

A: Telomeric repeat-binding factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,34612
Polymers51,1122
Non-polymers1,23410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3650 Å2
ΔGint-31 kcal/mol
Surface area20150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.398, 52.398, 146.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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, 53 molecules

#2: Chemical ChemComp-A1ITY / 4-[(3,5-dimethoxyphenyl)methoxy]naphthalene-1-sulfonic acid


Mass: 374.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / 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.: 48 / 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: 1.97 Å3/Da / Density % sol: 37.41 %
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: 2.07→49.33 Å / Num. obs: 13216 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 42.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.034 / Rrim(I) all: 0.125 / Net I/σ(I): 8.8 / Num. measured all: 186923 / Scaling rejects: 120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.1314.72.2551472710030.8550.6112.3380.8100
9.02-49.338.90.06319002140.9920.0210.06622.399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→37.05 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.197
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 638 4.85 %RANDOM
Rwork0.2229 ---
obs0.2251 13151 100 %-
Displacement parametersBiso max: 113.43 Å2 / Biso mean: 66.33 Å2 / Biso min: 46.19 Å2
Baniso -1Baniso -2Baniso -3
1--15.1848 Å20 Å20 Å2
2---15.1848 Å20 Å2
3---30.3696 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.07→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 39 48 1660
Biso mean--69.91 68 -
Num. residues----205
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d582SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes292HARMONIC5
X-RAY DIFFRACTIONt_it1656HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion224SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1302SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1656HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2232HARMONIC20.83
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion16.11
LS refinement shellResolution: 2.07→2.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.3656 20 4.71 %
Rwork0.4001 405 -
all0.3982 425 -
obs--99.76 %
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)
18.3154-2.21421.930800.01761.90950.3229-0.29260.13710.164-0.22140.03580.354-0.2648-0.10150.0633-0.10320.09250.0094-0.0403-0.0925.61556.60724.9075
23.1797-2.66541.22793.66150.6820-0.05150.3635-0.0240.3219-0.02520.1454-0.08810.20560.07660.0942-0.04890.00130.0096-0.0044-0.107618.6469.03713.3083
38.3154-0.41820.00860-0.58043.1667-0.17120.1019-0.02580.18090.0941-0.08590.0931-0.26790.07720.1031-0.05770.0793-0.0893-0.044-0.055813.10769.114914.9046
40.7127-0.0549-1.24735.6667-2.77894.82220.0674-0.13620.16050.216-0.0340.0669-0.45320.3651-0.03340.0517-0.05240.0438-0.0691-0.0658-0.03526.696615.255218.5068
51.3551-1.57822.33471.15090.12751.67990.0960.08390.20270.32370.22430.1017-0.1056-0.1433-0.32030.06230.03720.10620.0320.0616-0.040314.90762.240426.5697
61.94122.91041.01883.02741.04690.67270.0386-0.3621-0.0723-0.0405-0.01180.00160.29220.5128-0.02670.02430.02290.05480.0551-0.0053-0.08231.25914.75524.0891
71.83780.5422-0.02112.58160.05090.24350.0110.17890.13980.198-0.22640.0857-0.00540.35360.2154-0.0061-0.1520.02890.0957-0.053-0.121337.161816.65125.5664
84.1979-2.88552.91048.31540.69648.31550.0440.0225-0.34480.5442-0.0454-0.07470.23270.54420.0014-0.14840.022-0.08790.0622-0.074-0.148240.42725.745929.0121
98.31542.6362.82993.40562.65522.63920.0227-0.0044-0.0054-0.07870.05680.08360.54420.0699-0.07950.15140.0460.0098-0.1186-0.0253-0.090122.1219-3.146916.0368
100-0.78960.42642.1158-2.2770.71960.02320.0689-0.25450.3174-0.01230.14830.43370.0303-0.0109-0.0273-0.13530.04240.0036-0.0786-0.00285.3617-7.275-0.0066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|60 - 92}A60 - 92
2X-RAY DIFFRACTION2{A|93 - 111}A93 - 111
3X-RAY DIFFRACTION3{A|112 - 133}A112 - 133
4X-RAY DIFFRACTION4{A|134 - 160}A134 - 160
5X-RAY DIFFRACTION5{A|161 - 166}A161 - 166
6X-RAY DIFFRACTION6{A|167 - 187}A167 - 187
7X-RAY DIFFRACTION7{A|188 - 200}A188 - 200
8X-RAY DIFFRACTION8{A|201 - 232}A201 - 232
9X-RAY DIFFRACTION9{A|233 - 251}A233 - 251
10X-RAY DIFFRACTION10{A|252 - 268}A252 - 268

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