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- PDB-4joi: Crystal structure of the human telomeric Stn1-Ten1 complex -

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Basic information

Entry
Database: PDB / ID: 4joi
TitleCrystal structure of the human telomeric Stn1-Ten1 complex
Components
  • CST complex subunit STN1
  • CST complex subunit TEN1
KeywordsDNA BINDING PROTEIN / OB fold
Function / homology
Function and homology information


CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / telomere capping / intermediate filament cytoskeleton / telomeric DNA binding / negative regulation of telomere maintenance via telomerase ...CST complex / telomerase inhibitor activity / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / single-stranded telomeric DNA binding / Polymerase switching on the C-strand of the telomere / telomere capping / intermediate filament cytoskeleton / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance / positive regulation of DNA replication / fibrillar center / single-stranded DNA binding / chromosome, telomeric region / intracellular membrane-bounded organelle / nucleoplasm / nucleus
Similarity search - Function
CST complex subunit Ten1, animal and plant type / Telomere-capping, CST complex subunit / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins ...CST complex subunit Ten1, animal and plant type / Telomere-capping, CST complex subunit / CST complex subunit Stn1 / Stn1, C-terminal / CST complex subunit Stn1, wHTH1 motif superfamily / CST, complex subunit STN1, C terminal / Replication factor A protein-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CST complex subunit TEN1 / CST complex subunit STN1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsBryan, C. / Rice, C. / Harkisheimer, M. / Schultz, D. / Skordalakes, E.
CitationJournal: Plos One / Year: 2013
Title: Structure of the human telomeric stn1-ten1 capping complex.
Authors: Bryan, C. / Rice, C. / Harkisheimer, M. / Schultz, D.C. / Skordalakes, E.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Other
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Feb 28, 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: CST complex subunit STN1
B: CST complex subunit STN1
D: CST complex subunit TEN1
C: CST complex subunit TEN1


Theoretical massNumber of molelcules
Total (without water)65,7614
Polymers65,7614
Non-polymers00
Water2,972165
1
A: CST complex subunit STN1
D: CST complex subunit TEN1


Theoretical massNumber of molelcules
Total (without water)32,8812
Polymers32,8812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-14 kcal/mol
Surface area14990 Å2
MethodPISA
2
B: CST complex subunit STN1
C: CST complex subunit TEN1


Theoretical massNumber of molelcules
Total (without water)32,8812
Polymers32,8812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-16 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.613, 58.101, 87.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CST complex subunit STN1 / Oligonucleotide/oligosaccharide-binding fold-containing protein 1 / Suppressor of cdc thirteen homolog


Mass: 19139.922 Da / Num. of mol.: 2 / Fragment: Stn1 N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBFC1, STN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H668
#2: Protein CST complex subunit TEN1 / Protein telomeric pathways with STN1 homolog / Telomere length regulation protein TEN1 homolog


Mass: 13740.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEN1, C17orf106 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WV5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8 M AmSO4, 0.1 M citric acid pH 4.0 and 5% jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0076, 1.1000
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00761
21.11
ReflectionResolution: 2.05→20 Å / Num. all: 42636 / Num. obs: 42532 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6134 / Rsym value: 0.435 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 11.213 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.192 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24859 2102 4.9 %RANDOM
Rwork0.21078 ---
obs0.21267 40467 99.95 %-
all-42569 --
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: 54.429 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20 Å2
2--6.3 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 0 165 4376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024294
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9655804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73623.251203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81815786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9621538
X-RAY DIFFRACTIONr_chiral_restr0.0940.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213201
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 159 -
Rwork0.292 2700 -
obs--99.83 %
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)
12.40770.1805-0.42480.6918-0.22443.0342-0.00640.0920.09630.05450.0244-0.1081-0.12830.3852-0.0180.10960.01270.02080.12790.02720.1581-7.6435-11.121714.9033
22.8041-0.0384-0.45810.7390.31872.74590.0167-0.03150.163-0.02340.01940.0994-0.1044-0.3764-0.03620.13630.00050.02080.072-0.02310.162310.7973-12.6395-14.5685
31.9095-0.13270.06440.4015-1.23154.9276-0.04970.19480.30820.1675-0.02080.0161-0.7698-0.13660.07050.3213-0.0024-0.01810.05120.02940.24421.867-30.912-26.333
41.07770.082-0.08530.64380.61663.67420.01040.00030.23240.0418-0.05410.018-0.42940.05740.04370.21770.0162-0.01020.0292-0.04120.2106-18.956-27.8628.317
50.02930.0115-0.01410.04740.00010.0099-0.03480.01130.02410.00570.0346-0.00220.0264-0.00160.00020.0970.0047-0.00140.02290.00510.07392.412-18.022-0.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 183
2X-RAY DIFFRACTION2B22 - 183
3X-RAY DIFFRACTION3C2 - 119
4X-RAY DIFFRACTION4D2 - 119
5X-RAY DIFFRACTION5A201 - 245
6X-RAY DIFFRACTION5B201 - 244
7X-RAY DIFFRACTION5C201 - 241
8X-RAY DIFFRACTION5D201 - 235

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