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- PDB-6tzn: Structure of S. pombe telomerase accessory protein Pof8 C-termina... -

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Basic information

Entry
Database: PDB / ID: 6tzn
TitleStructure of S. pombe telomerase accessory protein Pof8 C-terminal domain
ComponentsProtein pof8
KeywordsRNA BINDING PROTEIN / RRM / LARP7 / Lsm binding
Function / homology
Function and homology information


nuclear RNA surveillance / telomerase catalytic core complex assembly / telomerase RNA stabilization / chromosome, telomeric repeat region / telomerase holoenzyme complex / telomerase RNA binding / telomere maintenance via telomerase / chromatin binding / nucleus / cytosol
Similarity search - Function
La-related protein 7 homolog, xRRM domain / xRRM domain / xRRM domain profile. / La protein, xRRM domain / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
NITRATE ION / La-related protein 7 homolog
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.35 Å
Model detailsPof8 xRRM
AuthorsBasu, R.S. / Cascio, D. / Eichhorn, C.D. / Feigon, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Citation
Journal: Rna Biol. / Year: 2021
Title: Structure of S. pombe telomerase protein Pof8 C-terminal domain is an xRRM conserved among LARP7 proteins.
Authors: Basu, R. / Eichhorn, C.D. / Cheng, R. / Peterson, R.D. / Feigon, J.
#1: Journal: Biorxiv / Year: 2019
Title: Structure of S. pombe telomerase accessory protein Pof8 C-terminal domain is conserved among LARP7 proteins
Authors: Basu, R.S. / Eichhorn, C.D. / Cheng, R.C. / Feigon, J.
History
DepositionAug 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Jul 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _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: Protein pof8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5222
Polymers14,4601
Non-polymers621
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint1 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.360, 57.360, 70.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein pof8


Mass: 14460.477 Da / Num. of mol.: 1 / Fragment: RNA Recognition Motif 2 - RRM2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pof8, SPAC17G6.17 / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13795
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 14% PEG 3350, 0.1 M NaNO3, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.35→49.675 Å / Num. obs: 29661 / % possible obs: 99.1 % / Redundancy: 4.59 % / Biso Wilson estimate: 19.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Χ2: 1.073 / Net I/σ(I): 16.09 / Num. measured all: 136156
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.394.2360.7411.959100217921480.7880.84498.6
1.39-1.424.6230.5352.929834213121270.9010.60399.8
1.42-1.464.6420.4073.789743210020990.9440.459100
1.46-1.514.5410.2825.249128201320100.9650.31999.9
1.51-1.564.3590.2016.788404193119280.9790.22999.8
1.56-1.614.7780.1658.878997188918830.9860.18599.7
1.61-1.674.7510.13210.618575181018050.9910.14899.7
1.67-1.744.6610.10612.968320179017850.9920.11999.7
1.74-1.824.3480.0815.597256168016690.9950.09199.3
1.82-1.914.760.06720.067616160516000.9950.07599.7
1.91-2.014.7570.05722.947264153315270.9970.06499.6
2.01-2.134.6850.0526.116896147814720.9970.05699.6
2.13-2.284.3980.04527.875994137313630.9970.05199.3
2.28-2.474.6560.04230.225885128612640.9980.04798.3
2.47-2.74.8310.03932.595749121011900.9980.04498.3
2.7-3.024.7070.03933.655060108810750.9980.04498.8
3.02-3.494.3580.03632.7840059579190.9970.04196
3.49-4.274.7630.03735.838208188020.9980.04198
4.27-6.044.5930.03635.2629126606340.9980.04196.1
6.04-49.6754.4270.0434.4915983943610.9980.04591.6

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PHASER1.3.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.35→49.675 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 2964 10 %
Rwork0.1629 26683 -
obs0.1662 29647 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.85 Å2 / Biso mean: 26.9107 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 1.35→49.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 4 78 1016
Biso mean--17.85 36.05 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005960
X-RAY DIFFRACTIONf_angle_d0.7131298
X-RAY DIFFRACTIONf_chiral_restr0.085143
X-RAY DIFFRACTIONf_plane_restr0.004167
X-RAY DIFFRACTIONf_dihedral_angle_d2.531590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3502-1.37230.30881390.2615125598
1.3723-1.3960.27461420.21481277100
1.396-1.42130.26281370.18611228100
1.4213-1.44870.2571400.17761263100
1.4487-1.47830.2051420.15811273100
1.4783-1.51040.19711410.13511267100
1.5104-1.54550.17331380.13621254100
1.5455-1.58420.19571390.13851257100
1.5842-1.6270.191390.12671250100
1.627-1.67490.15171410.13261272100
1.6749-1.7290.1761400.13911260100
1.729-1.79080.19331440.1431289100
1.7908-1.86250.19781390.1451125499
1.8625-1.94720.1931430.14881286100
1.9472-2.04990.19291420.15241284100
2.0499-2.17830.20361420.15281271100
2.1783-2.34650.17891410.1557127098
2.3465-2.58270.20171420.1715127599
2.5827-2.95630.2061430.1808128798
2.9563-3.72450.18611410.1762127597
3.7245-49.670.18811490.1638133695
Refinement TLS params.Method: refined / Origin x: -16.2144 Å / Origin y: 18.3329 Å / Origin z: -8.757 Å
111213212223313233
T0.1383 Å2-0.0118 Å20.0101 Å2-0.1235 Å20.0095 Å2--0.134 Å2
L3.7672 °2-0.3258 °20.35 °2-1.4048 °2-0.1815 °2--1.9469 °2
S-0.0428 Å °-0.0845 Å °-0.0855 Å °0.0485 Å °0.004 Å °-0.0571 Å °0.0348 Å °0.0461 Å °0.0301 Å °
Refinement TLS groupSelection details: all

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