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- PDB-6j67: Crystal structure of the compound 34 in a complex with TRF2 -

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Basic information

Entry
Database: PDB / ID: 6j67
TitleCrystal structure of the compound 34 in a complex with TRF2
Components
  • 3FB-PHE-B8R-LEU-5XU-PRO
  • Telomeric repeat-binding factor 2
KeywordsDNA BINDING PROTEIN / Telomere proteins / shelterin complex / TRF2 / Apollo / inhibitor
Function / homology
Function and homology information


axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere ...axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / positive regulation of nitric-oxide synthase activity / male germ cell nucleus / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / negative regulation of gene expression / positive regulation of gene expression / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus
Similarity search - Function
Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / 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 ...Telomere repeat-binding factor, dimerisation domain / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Homeobox-like domain superfamily / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Apollo peptide / Telomeric repeat-binding factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsChen, Y. / Yang, Y. / Lei, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473079 China
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Cyclic Peptidic Mimetics of Apollo Peptides Targeting Telomeric Repeat Binding Factor 2 (TRF2) and Apollo Interaction.
Authors: Chen, X. / Liu, L. / Chen, Y. / Yang, Y. / Yang, C.Y. / Guo, T. / Lei, M. / Sun, H. / Wang, S.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2
C: 3FB-PHE-B8R-LEU-5XU-PRO


Theoretical massNumber of molelcules
Total (without water)24,5882
Polymers24,5882
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.235, 95.235, 66.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Telomeric repeat-binding factor 2 / TRF2


Mass: 23724.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRF2 / Cell line (production host): Rosetta / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15554
#2: Protein/peptide 3FB-PHE-B8R-LEU-5XU-PRO


Type: Cyclic peptide / Class: Inhibitor / Mass: 863.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Apollo peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350, 100mM MgF, 100 mM Tris-HCl, PH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 20307 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 37.46 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Χ2: 2.323 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.12140.59419870.9310.1630.6170.84100
2.12-2.2114.20.45719700.9580.1250.4740.969100
2.21-2.3114.20.34219960.9760.0940.3541.271100
2.31-2.4314.20.27120000.9810.0740.2811.561100
2.43-2.5814.20.21720110.9890.060.2251.969100
2.58-2.7814.10.17519960.9920.0480.1822.603100
2.78-3.0613.60.13520330.9960.0380.143.126100
3.06-3.5112.70.10220340.9960.0290.1063.804100
3.51-4.4211.70.08120750.9980.0240.0844.37100
4.42-5012.10.05922050.9990.0170.0623.22199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.29 Å47.62 Å
Translation5.29 Å47.62 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6P

1h6p


Resolution: 2.05→31.593 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2216 947 4.76 %
Rwork0.2002 --
obs0.2014 19882 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.59 Å2 / Biso mean: 48.0454 Å2 / Biso min: 23.66 Å2
Refinement stepCycle: final / Resolution: 2.05→31.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 61 157 1876
Biso mean--56.6 52.22 -
Num. residues----203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031747
X-RAY DIFFRACTIONf_angle_d0.6982344
X-RAY DIFFRACTIONf_chiral_restr0.046264
X-RAY DIFFRACTIONf_plane_restr0.004297
X-RAY DIFFRACTIONf_dihedral_angle_d19.2021143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0502-2.15830.26681180.238226712789
2.1583-2.29340.24511400.221726322772
2.2934-2.47050.24461470.217726542801
2.4705-2.7190.21391290.216526852814
2.719-3.11210.22681220.225327012823
3.1121-3.91970.22991290.200127382867
3.9197-31.59680.2041620.17528543016
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)
14.5075-0.64670.7742.36220.09831.8722-0.0159-0.3037-0.2730.1832-0.1110.35210.0937-0.24190.18570.335-0.08320.06550.30690.01950.2918-13.5872-16.8863-27.8755
23.324-1.73011.79652.71620.45622.0868-0.2189-0.2651-0.1850.16020.04710.06170.0944-0.10560.1560.3078-0.0320.00750.30250.06160.2623-4.2949-14.2258-25.2188
34.29590.241.61892.5587-0.39053.5941-0.0674-0.14380.01910.1576-0.0542-0.3734-0.05910.40510.12560.27760.04920.00910.38530.08110.331814.3857-15.4033-15.9309
43.58160.21120.63073.32341.13091.29940.6336-0.6772-1.00950.11-0.22150.39650.7494-0.4557-0.36470.4556-0.14770.00450.38560.03630.5232-15.6902-27.7349-31.3019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 69 )A43 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 111 )A70 - 111
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 228 )A112 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 245 )A229 - 245

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