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- PDB-5doi: Crystal structure of Tetrahymena p45N and p19 -

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Basic information

Entry
Database: PDB / ID: 5doi
TitleCrystal structure of Tetrahymena p45N and p19
Components
  • Telomerase associated protein p45
  • Telomerase-associated protein 19
KeywordsDNA BINDING PROTEIN / telomerase / OB fold / Tetrahymena
Function / homologytelomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region / metal ion binding / Telomerase-associated protein of 19 kDa / Telomerase-associated protein of 45 kDa
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWan, B. / Tang, T. / Wu, J. / Lei, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The Tetrahymena telomerase p75-p45-p19 subcomplex is a unique CST complex
Authors: Wan, B. / Tang, T. / Upton, H. / Shuai, J. / Zhou, Y. / Li, S. / Chen, J. / Brunzelle, J.S. / Zeng, Z. / Collins, K. / Wu, J. / Lei, M.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase-associated protein 19
B: Telomerase-associated protein 19
C: Telomerase-associated protein 19
D: Telomerase-associated protein 19
E: Telomerase associated protein p45
F: Telomerase associated protein p45
G: Telomerase associated protein p45
H: Telomerase associated protein p45


Theoretical massNumber of molelcules
Total (without water)136,0198
Polymers136,0198
Non-polymers00
Water9,170509
1
A: Telomerase-associated protein 19
E: Telomerase associated protein p45


Theoretical massNumber of molelcules
Total (without water)34,0052
Polymers34,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-14 kcal/mol
Surface area12960 Å2
MethodPISA
2
B: Telomerase-associated protein 19
F: Telomerase associated protein p45


Theoretical massNumber of molelcules
Total (without water)34,0052
Polymers34,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-14 kcal/mol
Surface area13070 Å2
MethodPISA
3
C: Telomerase-associated protein 19
G: Telomerase associated protein p45


Theoretical massNumber of molelcules
Total (without water)34,0052
Polymers34,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-14 kcal/mol
Surface area13040 Å2
MethodPISA
4
D: Telomerase-associated protein 19
H: Telomerase associated protein p45


Theoretical massNumber of molelcules
Total (without water)34,0052
Polymers34,0052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.192, 125.828, 180.167
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Telomerase-associated protein 19 / p19


Mass: 19366.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP19 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2CVN7
#2: Protein
Telomerase associated protein p45 / p45


Mass: 14637.966 Da / Num. of mol.: 4 / Fragment: OB fold, UNP residues 2-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP45 / Plasmid: pMal / Production host: Escherichia coli (E. coli) / References: UniProt: Q6JXI5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 3.68 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 4.1 M LiCl, 50 mM HEPES sodium pH7.0, 10 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 2.2→125.83 Å / Num. obs: 99847 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.05 / Net I/σ(I): 10.8 / Num. measured all: 512980 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.2-2.465.10.5442.9145833283300.9380.26399.9
4.92-125.8350.05127.34535190300.9980.02599.6

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Processing

Software
NameVersionClassification
Aimless0.3.8data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.192 Å / FOM work R set: 0.7487 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.79 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 4861 5.03 %0
Rwork0.2258 91693 --
obs0.2323 96557 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.88 Å2 / Biso mean: 37.72 Å2 / Biso min: 17.25 Å2
Refinement stepCycle: final / Resolution: 2.2→44.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8104 0 0 509 8613
Biso mean---32.73 -
Num. residues----984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088313
X-RAY DIFFRACTIONf_angle_d1.16211148
X-RAY DIFFRACTIONf_chiral_restr0.0781259
X-RAY DIFFRACTIONf_plane_restr0.0041396
X-RAY DIFFRACTIONf_dihedral_angle_d16.3083112
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.23790.30152280.28454451467990
2.2379-2.27860.27542310.27654416464790
2.2786-2.32240.28822510.26974551480290
2.3224-2.36970.30952350.26914435467090
2.3697-2.42120.28082220.26944542476491
2.4212-2.47750.28352250.26474545477091
2.4775-2.53940.31212590.27094489474891
2.5394-2.6080.28922520.26584596484891
2.608-2.68460.2782390.26954482472191
2.6846-2.77120.28722330.26274615484892
2.7712-2.87010.31012490.26164517476692
2.8701-2.98480.28582280.25234620484893
2.9848-3.12040.26722580.24524594485292
3.1204-3.28450.22332520.23114611486393
3.2845-3.48970.23442180.21144670488893
3.4897-3.75830.23372320.19814663489593
3.7583-4.13490.20932440.19144680492494
4.1349-4.72940.20192490.1754675492494
4.7294-5.94430.26892440.21414754499894
5.9443-24.41720.29572750.24214787506294
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)
11.1727-0.4470.70281.4567-0.62342.26940.03630.014-0.0906-0.06910.0020.16510.1482-0.1541-0.02290.12060.0130.04540.20450.00230.415520.05144.73672.6663
21.8056-0.8128-0.89192.29160.88952.59550.13280.12950.0831-0.11820.0089-0.2372-0.45320.1429-0.0970.21860.01050.0440.2234-0.07610.347246.1274106.74345.0106
31.4360.6671.00382.06080.88382.46140.02440.0577-0.10720.033-0.0009-0.17170.18530.2035-0.02490.1505-0.00680.04680.20140.0060.347746.1445144.891284.8857
42.36241.0497-1.12492.9912-1.15472.85060.1243-0.15940.17430.10980.01240.1373-0.343-0.1679-0.09110.2285-0.01130.03920.20710.06610.289320.0384106.804187.5237
52.97320.04520.00382.5009-0.65635.4257-0.15-0.28530.01680.62650.1758-0.27910.13320.2283-0.0110.34530.1191-0.07860.2845-0.01780.317131.7182139.982427.9863
63.5222-0.10130.44974.0243-0.19145.3155-0.0625-0.2767-0.00620.53510.12570.45830.106-0.3251-0.01630.29860.10290.07120.21940.00410.373334.128110.992330.2171
73.0392-0.2092-0.20512.31090.61394.9902-0.14450.516-0.0642-0.61840.11120.30440.0953-0.2730.00780.3744-0.1014-0.05550.28070.00180.329634.4878140.197759.6929
83.23450.08380.13183.73190.67055.2621-0.09920.137-0.0688-0.46710.1174-0.45090.07170.0457-0.00670.289-0.08740.07290.1952-0.00190.353331.5182111.502462.129
90.1002-0.0053-0.00070.00610.0303-0.24310.0246-0.00530.03540.0086-0.0163-0.0009-0.002-0.0242-0.02360.2512-0.0105-0.01380.1980.00670.470830.6505127.850747.8317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 7:162A7 - 162
2X-RAY DIFFRACTION2CHAIN B AND RESID 7:162B7 - 162
3X-RAY DIFFRACTION3CHAIN C AND RESID 7:162C7 - 162
4X-RAY DIFFRACTION4CHAIN D AND RESID 7:162D7 - 162
5X-RAY DIFFRACTION5CHAIN E AND RESID 4:125E4 - 125
6X-RAY DIFFRACTION6CHAIN F AND RESID 4:125F4 - 125
7X-RAY DIFFRACTION7CHAIN G AND RESID 4:125G4 - 125
8X-RAY DIFFRACTION8CHAIN H AND RESID 4:125H4 - 125
9X-RAY DIFFRACTION9( CHAIN A AND RESID 201:313 ) OR ( CHAIN C AND RESID 201:308 ) OR ( CHAIN B AND RESID 201:266 ) OR ( CHAIN E AND RESID 201:229 ) OR ( CHAIN D AND RESID 201:307 ) OR ( CHAIN G AND RESID 201:230 ) OR ( CHAIN F AND RESID 201:227 ) OR ( CHAIN H AND RESID 201:229 )

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