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- PDB-2i46: Crystal structure of human TPP1 -

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Basic information

Entry
Database: PDB / ID: 2i46
TitleCrystal structure of human TPP1
ComponentsAdrenocortical dysplasia protein homolog
KeywordsPROTEIN BINDING / TPP1 / OB fold / POT1 binding
Function / homology
Function and homology information


positive regulation of single-stranded telomeric DNA binding / telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / telomere capping / Telomere C-strand (Lagging Strand) Synthesis ...positive regulation of single-stranded telomeric DNA binding / telomere assembly / segmentation / urogenital system development / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / Telomere C-strand synthesis initiation / telomere capping / 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 / 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 / telomere maintenance via telomerase / Telomere Extension By 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 / positive regulation of telomere maintenance via telomerase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere maintenance / Meiotic synapsis / 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
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #960 / Shelterin complex subunit TPP1/Est3 / Shelterin complex subunit, TPP1/ACD / Adrenocortical dysplasia protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Adrenocortical dysplasia protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsWang, F. / Podell, E.R. / Zaug, A.J. / Yang, Y.T. / Baciu, P. / Else, T. / Hammer, G.D. / Cech, T.R. / Lei, M.
CitationJournal: Nature / Year: 2007
Title: The POT1-TPP1 telomere complex is a telomerase processivity factor.
Authors: Wang, F. / Podell, E.R. / Zaug, A.J. / Yang, Y. / Baciu, P. / Cech, T.R. / Lei, M.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Adrenocortical dysplasia protein homolog
B: Adrenocortical dysplasia protein homolog


Theoretical massNumber of molelcules
Total (without water)35,1172
Polymers35,1172
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-14 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.246, 117.246, 171.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-295-

HOH

21A-297-

HOH

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Components

#1: Protein Adrenocortical dysplasia protein homolog / POT1 and TIN2-interacting protein


Mass: 17558.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACD, PIP1, PTOP / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q96AP0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 4.2 Å3/Da / Density % sol: 70.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 3.5 M Sodium formate, 0.1 M sodium citrate, pH 5.6, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 17184 / Num. obs: 16372 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 2.7
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.3 / % possible all: 81.7

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2509 1626 RANDOM
Rwork0.2135 --
all-16800 -
obs-16336 -
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 88 2304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005891
X-RAY DIFFRACTIONc_angle_deg1.28141
X-RAY DIFFRACTIONc_dihedral_angle_d24.23687
X-RAY DIFFRACTIONc_improper_angle_d0.8137

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