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- PDB-5un7: Structure of the human POT1-TPP1 telomeric complex -

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Basic information

Entry
Database: PDB / ID: 5un7
TitleStructure of the human POT1-TPP1 telomeric complex
Components
  • Adrenocortical dysplasia protein homolog
  • Protection of telomeres protein 1
KeywordsPROTEIN BINDING / Telomeric DNA binding complex / maintains telomere integrity / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / protection from non-homologous end joining at telomere / regulation of double-strand break repair via nonhomologous end joining ...positive regulation of DNA strand elongation / positive regulation of telomeric D-loop disassembly / G-rich single-stranded DNA binding / telomere assembly / segmentation / urogenital system development / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / protection from non-homologous end joining at telomere / regulation of double-strand break repair via nonhomologous end joining / telomerase inhibitor activity / DEAD/H-box RNA helicase binding / regulation of establishment of protein localization to telomere / establishment of protein localization to telomere / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / single-stranded telomeric DNA binding / 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 / telomerase holoenzyme complex / embryonic limb morphogenesis / protein localization to chromosome, telomeric region / telomeric DNA binding / 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 / DNA polymerase binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of telomere maintenance via telomerase / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / skeletal system development / intracellular protein transport / DNA Damage/Telomere Stress Induced Senescence / chromosome, telomeric region / nuclear body / protein-containing complex binding / nucleoplasm
Similarity search - Function
: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 ...: / Protection of telomeres protein 1 (POT1), C-terminal insertion domain / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Adrenocortical dysplasia protein homolog / Protection of telomeres protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsRice, C. / Doukov, T. / Skordalakes, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA201312 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088332-03 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA10815 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural and functional analysis of the human POT1-TPP1 telomeric complex.
Authors: Rice, C. / Shastrula, P.K. / Kossenkov, A.V. / Hills, R. / Baird, D.M. / Showe, L.C. / Doukov, T. / Janicki, S. / Skordalakes, E.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1656
Polymers43,9822
Non-polymers1834
Water9,620534
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-39 kcal/mol
Surface area17800 Å2
MethodPISA
2
A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules

A: Protection of telomeres protein 1
B: Adrenocortical dysplasia protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,33012
Polymers87,9654
Non-polymers3658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area13300 Å2
ΔGint-88 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.530, 99.530, 122.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-922-

HOH

21A-965-

HOH

31A-1240-

HOH

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Components

#1: Protein Protection of telomeres protein 1 / hPot1 / POT1-like telomere end-binding protein


Mass: 34786.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUX5
#2: Protein Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 9195.318 Da / Num. of mol.: 1 / Fragment: UNP residues 255-337
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) / References: UniProt: Q96AP0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.4 M KCl, 50 mM K/Na Tartrate, 20 mM BaCl2, and 0.1 M Sodium Citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.1→38.6 Å / Num. obs: 68409 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 22.8
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 20 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5044 / CC1/2: 0.85 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.842 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22199 1821 5 %RANDOM
Rwork0.18241 ---
obs0.18432 34593 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å2-0 Å2
2--0.16 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 4 534 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9723931
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05525.289121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95415512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7151510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9433.8321448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2245.7241805
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7024.0641455
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.10533.9924889
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 131 -
Rwork0.242 2473 -
obs--100 %

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