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- PDB-4jqf: Structure of the C-terminal domain of human telomeric Stn1 -

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Basic information

Entry
Database: PDB / ID: 4jqf
TitleStructure of the C-terminal domain of human telomeric Stn1
ComponentsCST complex subunit STN1
KeywordsDNA BINDING PROTEIN / Wing-helix-turn-helix (wHTH) motif / Protein binding / Pol alpha / Ctc1
Function / homology
Function and homology information


CST complex / 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 ...CST complex / 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, Suppressor of Cdc13 homolog, complex subunit STN1, N-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...CST, Suppressor of Cdc13 homolog, complex subunit STN1, N-terminal domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CST complex subunit STN1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBryan, C.F. / Rice, C.T. / 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 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CST complex subunit STN1


Theoretical massNumber of molelcules
Total (without water)20,4731
Polymers20,4731
Non-polymers00
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.805, 76.572, 114.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsheterotrimer

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Components

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


Mass: 20473.260 Da / Num. of mol.: 1 / Fragment: unp residues 191-368
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 8.5
Details: 1.6 M Ammonium phosphate dibasic, 100 mM Tris, 3% Ethylene glycol, pH 8.5, VAPOR DIFFUSION, Microbatch Crystallization, temperature 289.15K

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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: Dec 5, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00761
21.11
ReflectionResolution: 1.6→20 Å / Num. all: 34343 / Num. obs: 34343 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 13.8
Reflection shellResolution: 1.6→1.641 Å / Redundancy: 4 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.486 / % 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: 1.6→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.843 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21899 1718 5 %RANDOM
Rwork0.19744 ---
obs0.19852 32625 99.9 %-
all-32625 --
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: 24.118 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.34 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 0 166 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021374
X-RAY DIFFRACTIONr_angle_refined_deg0.9381.9661853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5065166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02125.29468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67915258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.883156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211019
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 116 -
Rwork0.333 2118 -
obs--99.33 %
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)
10.07750.2033-0.20571.0216-0.47740.57270.01480.00740.01280.1097-0.00020.0093-0.02320.0014-0.01460.01460.00350.0020.03220.02770.0317-2.104633.201393.9258
20.15150.3396-0.30230.9639-0.60470.63280.02890.0080.00850.0876-0.01630.0132-0.0575-0.0209-0.01260.01420.0080.00880.02210.02260.0326-2.50433.850890.8656
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A190 - 368
2X-RAY DIFFRACTION2A401 - 566

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