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- PDB-5ugw: STRUCTURE OF THE HUMAN TELOMERASE THUMB DOMAIN -

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Basic information

Entry
Database: PDB / ID: 5ugw
TitleSTRUCTURE OF THE HUMAN TELOMERASE THUMB DOMAIN
ComponentsTelomerase reverse transcriptase
KeywordsTRANSFERASE / Telomerase / reverse transcriptase / thumb domain
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / nuclear telomere cap complex / siRNA processing / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / RNA-templated transcription / DNA biosynthetic process / telomeric DNA binding / positive regulation of stem cell proliferation / mitochondrial nucleoid / negative regulation of cellular senescence / Telomere Extension By Telomerase / replicative senescence / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / telomere maintenance via telomerase / RNA-directed DNA polymerase activity / negative regulation of endothelial cell apoptotic process / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of nitric-oxide synthase activity / positive regulation of D-glucose import / mitochondrion organization / Formation of the beta-catenin:TCF transactivating complex / transcription coactivator binding / regulation of protein stability / PML body / positive regulation of miRNA transcription / RNA-directed DNA polymerase / telomerase activity / protein import into nucleus / positive regulation of angiogenesis / positive regulation of protein binding / protein-folding chaperone binding / heart development / cellular response to hypoxia / negative regulation of neuron apoptotic process / tRNA binding / chromosome, telomeric region / nuclear speck / negative regulation of gene expression / RNA-directed RNA polymerase activity / nucleolus / protein homodimerization activity / DNA binding / RNA binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
GLUTATHIONE / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.31 Å
AuthorsSkordalakes, E. / Hoffman, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA201312 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA10815 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Analysis Reveals the Deleterious Effects of Telomerase Mutations in Bone Marrow Failure Syndromes.
Authors: Hoffman, H. / Rice, C. / Skordalakes, E.
History
DepositionJan 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1083
Polymers19,4931
Non-polymers6152
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.425, 92.425, 50.178
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1308-

HOH

21A-1323-

HOH

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Components

#1: Protein Telomerase reverse transcriptase / HEST2 / Telomerase catalytic subunit / Telomerase-associated protein 2 / TP2


Mass: 19492.941 Da / Num. of mol.: 1 / Fragment: UNP residues 961-1132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERT, EST2, TCS1, TRT / Production host: Escherichia coli (E. coli) / References: UniProt: O14746, RNA-directed DNA polymerase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris 8.5 0.8 M LiSo4 10 mM GSH/GSSG 3% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.64
11-h,-k,l20.36
ReflectionResolution: 2.3→26.68 Å / Num. obs: 10654 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 0.999 / Net I/σ(I): 18.68
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 10.25 % / Mean I/σ(I) obs: 2.19 / Num. unique all: 813 / Num. unique obs: 813 / CC1/2: 0.7 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→26.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.666 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.209 522 4.7 %RANDOM
Rwork0.19729 ---
obs0.19781 10564 99.94 %-
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: 61.161 Å2
Baniso -1Baniso -2Baniso -3
1-19.92 Å2-0 Å20 Å2
2--19.92 Å20 Å2
3----39.84 Å2
Refinement stepCycle: 1 / Resolution: 2.31→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 40 24 1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.9981759
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1965157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22122.08348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6281510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021949
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_it2.425.945631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.8798.9787
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7186.179669
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.91150.5631929
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: 2.31→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 40 -
Rwork0.304 752 -
obs--99.87 %

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