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- PDB-5xyf: Crystal structure of the human TIN2-TPP1-TRF2 telomeric complex -

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Basic information

Entry
Database: PDB / ID: 5xyf
TitleCrystal structure of the human TIN2-TPP1-TRF2 telomeric complex
Components
  • Adrenocortical dysplasia protein homolog
  • TERF1-interacting nuclear factor 2
  • Telomeric repeat-binding factor 2
KeywordsPROTEIN BINDING / telomere / shelterin complex
Function / homology
Function and homology information


regulation of telomere maintenance via telomere lengthening / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / perinucleolar chromocenter / negative regulation of telomere maintenance via recombination / telomeric loop formation / telomere assembly / segmentation / negative regulation of telomere capping / urogenital system development ...regulation of telomere maintenance via telomere lengthening / axonal transport of messenger ribonucleoprotein complex / negative regulation of telomere single strand break repair / perinucleolar chromocenter / negative regulation of telomere maintenance via recombination / telomeric loop formation / telomere assembly / segmentation / negative regulation of telomere capping / urogenital system development / protection from non-homologous end joining at telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / regulation of establishment of protein localization to telomere / negative regulation of telomere maintenance / negative regulation of t-circle formation / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / shelterin complex / telomeric D-loop disassembly / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / Polymerase switching on the C-strand of the telomere / telomerase holoenzyme complex / Processive synthesis on the C-strand of the telomere / embryonic limb morphogenesis / Removal of the Flap Intermediate from the C-strand / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric repeat DNA binding / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / negative regulation of cellular senescence / Telomere Extension By Telomerase / telomere maintenance via telomerase / DNA polymerase binding / 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 / male germ cell nucleus / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / negative regulation of epithelial cell proliferation / nuclear matrix / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / axon / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus
Similarity search - Function
TERF1-interacting nuclear factor 2, N-terminal domain / TERF1-interacting nuclear factor 2 / TERF1-interacting nuclear factor 2 N-terminus / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Telomeric repeat-binding factor 1/2 ...TERF1-interacting nuclear factor 2, N-terminal domain / TERF1-interacting nuclear factor 2 / TERF1-interacting nuclear factor 2 N-terminus / Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Adrenocortical dysplasia protein / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / 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 2 / Adrenocortical dysplasia protein homolog / TERF1-interacting nuclear factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.202 Å
AuthorsHu, C. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation31470737 China
Ministry of Science and Technology of China2013CB910401 China
CitationJournal: Cell Res. / Year: 2017
Title: Structural and functional analyses of the mammalian TIN2-TPP1-TRF2 telomeric complex.
Authors: Hu, C. / Rai, R. / Huang, C. / Broton, C. / Long, J. / Xu, Y. / Xue, J. / Lei, M. / Chang, S. / Chen, Y.
History
DepositionJul 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TERF1-interacting nuclear factor 2
C: Telomeric repeat-binding factor 2
B: Adrenocortical dysplasia protein homolog


Theoretical massNumber of molelcules
Total (without water)29,8343
Polymers29,8343
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, A,B,C chains form a heterotrimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-37 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.222, 112.258, 121.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TERF1-interacting nuclear factor 2 / TRF1-interacting nuclear protein 2


Mass: 23180.242 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TINF2, TIN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BSI4
#2: Protein/peptide Telomeric repeat-binding factor 2 / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 2146.553 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 392-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15554
#3: Protein/peptide Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 4506.760 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 510-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP, TINT1, TPP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96AP0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsNature variant at this position

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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: 2.64 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 0.2M Magnesium chloride, 25% PEG 3350, 2mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16609 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.18 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.053 / Rrim(I) all: 0.135 / Χ2: 1.347 / Net I/σ(I): 5.3 / Num. measured all: 106155
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.30.5718230.8750.2440.6220.54499.9
2.24-2.286.20.4627970.9040.2010.5040.5799.7
2.28-2.325.80.4538380.90.2070.50.61299.8
2.32-2.376.40.417890.9390.1760.4470.617100
2.37-2.426.60.3368350.9540.1390.3640.657100
2.42-2.486.70.3238120.9610.1330.350.722100
2.48-2.546.60.2748170.9710.1130.2970.7599.9
2.54-2.616.60.2478260.9690.1030.2680.821100
2.61-2.696.50.228140.980.0920.2390.82299.9
2.69-2.776.30.2068230.960.090.2260.88499.9
2.77-2.875.90.1888200.9670.0850.2071.03899.9
2.87-2.996.80.1718090.980.070.1851.08199.8
2.99-3.126.80.1528380.9830.0630.1651.25699.9
3.12-3.296.70.1358290.9880.0560.1471.432100
3.29-3.496.60.1148320.9910.0480.1241.71999.8
3.49-3.7660.1088420.9860.0480.1182.31499.9
3.76-4.146.80.1018380.9920.0420.112.4100
4.14-4.746.50.0898530.9950.0380.0972.799100
4.74-5.976.10.0888580.9940.0390.0972.30299.9
5.97-5060.089160.9940.0360.0883.32899.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
SHARPphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.202→32.791 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 828 5.07 %
Rwork0.1955 15513 -
obs0.197 16341 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.1 Å2 / Biso mean: 49.4165 Å2 / Biso min: 25.07 Å2
Refinement stepCycle: final / Resolution: 2.202→32.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 72 1908
Biso mean---50.52 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041876
X-RAY DIFFRACTIONf_angle_d0.62538
X-RAY DIFFRACTIONf_chiral_restr0.033282
X-RAY DIFFRACTIONf_plane_restr0.005322
X-RAY DIFFRACTIONf_dihedral_angle_d14.6831144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2025-2.34040.30151350.22622538267399
2.3404-2.52110.22251420.213125222664100
2.5211-2.77470.2211380.202825682706100
2.7747-3.17590.2761350.218925762711100
3.1759-4.00020.21771490.187625842733100
4.0002-32.79480.20391290.18127252854100
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)
11.1674-1.90720.92575.12571.65172.32570.15470.2247-0.3165-0.2536-0.16080.12840.1441-0.18240.05390.25410.0032-0.01270.2778-0.02010.299517.398632.363112.8725
24.0527-3.4274.01355.6701-4.99047.3748-0.2276-0.62810.03220.61940.40330.2354-0.3195-0.8120.23780.29960.0147-0.00170.229-0.0020.269811.338141.817518.9719
34.3202-1.48043.12956.5306-4.10513.9454-0.22750.0834-0.3012-0.07730.11350.4630.4952-0.5977-0.19710.2832-0.01590.05320.2383-0.05730.32490.962845.98435.7329
42.19240.7391-0.88134.0606-1.81362.4914-0.7586-0.9708-0.65550.2353-0.1636-0.49711.106-1.14110.82390.6301-0.03140.10640.6295-0.03080.69482.764338.156926.8325
52.3537-1.2074-1.48585.0695-4.26364.2879-0.3968-0.63920.02410.83180.33930.3671-0.8032-0.4744-0.02930.38040.02680.09710.3634-0.0410.37771.70250.234721.3262
67.8357-5.99586.87174.7808-5.82596.0415-0.4438-0.32060.24010.81430.0539-0.3248-0.53310.21650.50530.4344-0.0397-0.04380.2964-0.02620.39497.734659.79169.4372
74.7399-3.0883.5629.2919-3.40683.8255-0.3720.16860.38780.36490.1934-0.2617-0.29540.38880.21740.2479-0.0311-0.01860.1711-0.04210.256621.74339.473120.3258
80.38990.17940.09210.14930.03460.5766-1.36780.8451-0.2415-0.12860.4284-0.77781.74991.6946-0.2650.67350.0906-0.0610.4654-0.19720.80230.194321.63217.287
97.32131.11614.52947.40410.36875.0737-0.1614-0.55260.87260.1614-0.73330.7724-0.0428-1.03080.17340.38650.05020.03510.2895-0.08360.363926.033418.84714.7391
100.36050.51030.07871.95461.98787.2975-0.1031-1.00230.4486-1.0691-0.00590.7109-1.26420.0878-0.30.5228-0.00870.03820.3773-0.07490.592828.773422.378-2.0949
110.60710.95750.40468.24693.82455.4490.2855-0.26160.00210.2269-0.1493-0.9388-0.01730.5017-0.32040.28160.0081-0.0020.4906-0.07180.565131.5331.596913.8111
127.2584-0.1519-2.30276.92220.69253.614-0.6698-1.53040.56641.15170.4365-0.0957-0.6172-0.0263-0.3770.54740.0407-0.02160.4359-0.10410.465911.158252.407324.4011
133.0886-3.21541.79038.4619-6.60446.5008-0.1390.2775-0.23710.3955-0.1978-0.1107-0.26820.64720.31460.5412-0.145-0.01680.37690.01460.643716.387420.934823.6696
144.9168-0.5571-2.37176.361.55667.74570.81590.9473-0.9445-0.8238-0.83410.05620.5766-0.1609-0.29690.43490.126-0.1050.3869-0.08290.328817.803126.96415.2607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 44 )A5 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 71 )A45 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 86 )A72 - 86
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 100 )A87 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 123 )A101 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 140 )A124 - 140
7X-RAY DIFFRACTION7chain 'A' and (resid 141 through 161 )A141 - 161
8X-RAY DIFFRACTION8chain 'A' and (resid 162 through 168 )A162 - 168
9X-RAY DIFFRACTION9chain 'A' and (resid 169 through 177 )A169 - 177
10X-RAY DIFFRACTION10chain 'A' and (resid 178 through 186 )A178 - 186
11X-RAY DIFFRACTION11chain 'A' and (resid 187 through 199 )A187 - 199
12X-RAY DIFFRACTION12chain 'C' and (resid 355 through 366 )C355 - 366
13X-RAY DIFFRACTION13chain 'B' and (resid 509 through 521 )B509 - 521
14X-RAY DIFFRACTION14chain 'B' and (resid 522 through 533 )B522 - 533

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