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- PDB-5y5a: Crystal structure of Est1 and Cdc13 -

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Basic information

Entry
Database: PDB / ID: 5y5a
TitleCrystal structure of Est1 and Cdc13
Components
  • KLLA0F20702p
  • KLLA0F20922p
KeywordsPROTEIN BINDING / telomerase / telomere / protein-protein complex
Function / homology
Function and homology information


telomere maintenance / chromosome, telomeric region / DNA binding
Similarity search - Function
Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Est1 DNA/RNA binding domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 ...Telomerase activating protein Est1-like, N-terminal / Telomerase activating protein Est1 / DNA/RNA-binding domain, Est1-type / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Est1 DNA/RNA binding domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
KLLA0F20922p / KLLA0F20702p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.206 Å
AuthorsChen, H. / Xue, J. / Wu, J. / Lei, M.
CitationJournal: Cell / Year: 2018
Title: Structural Insights into Yeast Telomerase Recruitment to Telomeres
Authors: Chen, H. / Xue, J. / Churikov, D. / Hass, E.P. / Shi, S. / Lemon, L.D. / Luciano, P. / Bertuch, A.A. / Zappulla, D.C. / Geli, V. / Wu, J. / Lei, M.
History
DepositionAug 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0F20702p
B: KLLA0F20922p


Theoretical massNumber of molelcules
Total (without water)69,4002
Polymers69,4002
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.611, 41.726, 147.060
Angle α, β, γ (deg.)90.000, 97.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KLLA0F20702p


Mass: 66373.492 Da / Num. of mol.: 1 / Fragment: UNP residues 2-600 / Mutation: 384-415 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F20702g / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CJ80
#2: Protein/peptide KLLA0F20922p


Mass: 3026.250 Da / Num. of mol.: 1 / Fragment: UNP residues 213-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0_F20922g / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CJ70
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.28 Å3/Da / Density % sol: 45.97 % / Mosaicity: 1.853 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 7 / Details: 0.2 M potassium chloride, and 20% PEG3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL18U110.9786
SYNCHROTRONSSRF BL19U120.9786
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELDec 30, 2014
DECTRIS PILATUS 6M2PIXELDec 30, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
21
ReflectionResolution: 2.2→50 Å / Num. obs: 30712 / % possible obs: 91.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 45.85 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Χ2: 1.015 / Net I/σ(I): 5.5 / Num. measured all: 194302
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.80.59430870.8380.2620.6520.52893.6
2.28-2.376.10.45729980.8930.1960.4990.5790.8
2.37-2.486.50.36930800.9330.1540.4010.63792.6
2.48-2.616.40.27330810.9620.1150.2970.74292.3
2.61-2.776.20.21930140.9680.0930.2390.85390.6
2.77-2.996.40.16829700.9810.0710.1831.06989.9
2.99-3.296.50.13330070.9890.0550.1441.28890.4
3.29-3.766.30.10529600.9910.0440.1151.56488.1
3.76-4.746.40.09231740.9910.0380.11.46394.1
4.74-506.60.0733410.9960.0290.0761.32795.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.206→40.856 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2245 1534 5 %
Rwork0.1756 29150 -
obs0.178 30684 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 254.14 Å2 / Biso mean: 65.8954 Å2 / Biso min: 29.15 Å2
Refinement stepCycle: final / Resolution: 2.206→40.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 0 73 4442
Biso mean---53.82 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054459
X-RAY DIFFRACTIONf_angle_d0.8525992
X-RAY DIFFRACTIONf_chiral_restr0.034664
X-RAY DIFFRACTIONf_plane_restr0.004751
X-RAY DIFFRACTIONf_dihedral_angle_d12.491679
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.206-2.27720.29031450.23552625277092
2.2772-2.35860.251390.21152566270589
2.3586-2.4530.27991260.19722689281593
2.453-2.56460.25171250.1972690281594
2.5646-2.69980.23891390.19282605274491
2.6998-2.86890.2691370.20392552268988
2.8689-3.09040.25451380.20892612275091
3.0904-3.40120.25161360.22612274890
3.4012-3.89310.22611630.17422530269388
3.8931-4.90350.16821260.1462814294096
4.9035-40.86350.21451600.15642855301595
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)
11.14880.1868-0.14661.615-0.51292.25520.0238-0.37360.07680.21840.0072-0.0492-0.03660.1743-0.03650.35540.0430.00180.3414-0.04530.333139.510923.459838.6945
21.7288-0.75732.77720.4566-1.77066.920.13870.2427-0.4716-0.79050.4815-0.16481.54750.6119-0.6810.88170.01430.04040.54130.04750.773754.32113.427729.6491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA7 - 600
2X-RAY DIFFRACTION2chain BB213 - 238

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