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- PDB-5dfm: Structure of Tetrahymena telomerase p19 fused to MBP -

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Basic information

Entry
Database: PDB / ID: 5dfm
TitleStructure of Tetrahymena telomerase p19 fused to MBP
ComponentsMaltose-binding periplasmic protein,Telomerase-associated protein 19
KeywordsNUCLEAR PROTEIN / Telomerase / P19 / CST complex / Ten1 / OB-fold / Oligonucleotide Binding Fold
Function / homology
Function and homology information


telomerase holoenzyme complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / telomere maintenance via telomerase / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...telomerase holoenzyme complex / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / telomere maintenance via telomerase / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / chromosome, telomeric region / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Telomerase-associated protein of 19 kDa / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Tetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
Model detailsTelomerase protein P19
AuthorsChan, H. / Cascio, D. / Sawaya, M.R. / Feigon, J.
CitationJournal: Science / Year: 2015
Title: Structure of Tetrahymena telomerase reveals previously unknown subunits, functions, and interactions.
Authors: Jiansen Jiang / Henry Chan / Darian D Cash / Edward J Miracco / Rachel R Ogorzalek Loo / Heather E Upton / Duilio Cascio / Reid O'Brien Johnson / Kathleen Collins / Joseph A Loo / Z Hong Zhou / Juli Feigon /
Abstract: Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the ...Telomerase helps maintain telomeres by processive synthesis of telomere repeat DNA at their 3'-ends, using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). We report the cryo-electron microscopy structure of Tetrahymena telomerase at ~9 angstrom resolution. In addition to seven known holoenzyme proteins, we identify two additional proteins that form a complex (TEB) with single-stranded telomere DNA-binding protein Teb1, paralogous to heterotrimeric replication protein A (RPA). The p75-p45-p19 subcomplex is identified as another RPA-related complex, CST (CTC1-STN1-TEN1). This study reveals the paths of TER in the TERT-TER-p65 catalytic core and single-stranded DNA exit; extensive subunit interactions of the TERT essential N-terminal domain, p50, and TEB; and other subunit identities and structures, including p19 and p45C crystal structures. Our findings provide structural and mechanistic insights into telomerase holoenzyme function.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Telomerase-associated protein 19
B: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,01720
Polymers119,7992
Non-polymers2,21818
Water1,42379
1
A: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8148
Polymers59,9001
Non-polymers9157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,20312
Polymers59,9001
Non-polymers1,30311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Maltose-binding periplasmic protein,Telomerase-associated protein 19
B: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules

A: Maltose-binding periplasmic protein,Telomerase-associated protein 19
B: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules

A: Maltose-binding periplasmic protein,Telomerase-associated protein 19
B: Maltose-binding periplasmic protein,Telomerase-associated protein 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,05160
Polymers359,3986
Non-polymers6,65354
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_478z-1/2,-x+5/2,-y+31
crystal symmetry operation12_785-y+5/2,-z+3,x+1/21
Buried area31540 Å2
ΔGint-661 kcal/mol
Surface area110650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.600, 150.600, 150.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALAchain AAA1 - 5271 - 527
2LEULEUchain BBB1 - 5221 - 522

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Components

#1: Protein Maltose-binding periplasmic protein,Telomerase-associated protein 19 / MBP / MMBP / Maltodextrin-binding protein


Mass: 59899.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Tetrahymena thermophila (eukaryote)
Gene: malE, TAP19 / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEY0, UniProt: D2CVN7, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12 mg/ml MBP-P19 protein, 0.1 M Sodium Acetate, 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→86.949 Å / Num. obs: 50601 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.63 % / Biso Wilson estimate: 40.16 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.122 / Χ2: 1.074 / Net I/σ(I): 19.38 / Num. measured all: 993498
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.3618.810.91.0333.4369209372736791.06298.7
2.36-2.430.9380.9114.0766308361436140.937100
2.43-2.50.9610.6865.373775352735250.70399.9
2.5-2.570.9680.5736.2471033340033990.588100
2.57-2.660.9750.4897.4468624331633160.502100
2.66-2.750.9830.3999.0965239320132000.409100
2.75-2.850.9870.34210.6862290313331320.351100
2.85-2.970.9890.28412.5853992297529740.292100
2.97-3.10.9930.22216.259659285128510.227100
3.1-3.250.9960.16820.4956688273627350.172100
3.25-3.430.9970.13524.5453080263726350.13999.9
3.43-3.640.9980.10730.4147631246324620.11100
3.64-3.890.9980.09132.7440129232623260.094100
3.89-4.20.9990.07838.9643198220322030.08100
4.2-4.60.9990.06943.1938425198919890.071100
4.6-5.150.9990.06544.1435037183318330.067100
5.15-5.940.9990.06440.9528724161916190.066100
5.94-7.280.9990.05546.1428301138113810.056100
7.28-10.290.9990.04350.6520765108810880.044100
10.29-86.94910.03851.51113916436400.03999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata scaling
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.301→86.949 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 5057 10 %Random selection
Rwork0.1748 45512 --
obs0.1799 50569 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.41 Å2 / Biso mean: 45.4775 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 2.301→86.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7773 0 127 80 7980
Biso mean--69.24 37.11 -
Num. residues----1015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088082
X-RAY DIFFRACTIONf_angle_d1.14311006
X-RAY DIFFRACTIONf_chiral_restr0.0461220
X-RAY DIFFRACTIONf_plane_restr0.0061409
X-RAY DIFFRACTIONf_dihedral_angle_d13.3922838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4468X-RAY DIFFRACTION5.755TORSIONAL
12B4468X-RAY DIFFRACTION5.755TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3012-2.32730.31371610.22661450161197
2.3273-2.35470.30761700.206515351705100
2.3547-2.38340.28041650.210214801645100
2.3834-2.41360.30861660.20715061672100
2.4136-2.44540.30731710.208315351706100
2.4454-2.47890.28181640.208314771641100
2.4789-2.51430.2751680.204915161684100
2.5143-2.55180.28221680.214415141682100
2.5518-2.59170.26981680.209715031671100
2.5917-2.63420.30041670.201515041671100
2.6342-2.67960.27251640.207214741638100
2.6796-2.72830.31261680.207115201688100
2.7283-2.78080.2741700.222615261696100
2.7808-2.83760.30341690.216315221691100
2.8376-2.89930.3161650.216214861651100
2.8993-2.96670.29151680.213515101678100
2.9667-3.04090.26781680.21215121680100
3.0409-3.12320.29391670.202615031670100
3.1232-3.21510.27871700.197915211691100
3.2151-3.31880.22221660.199714981664100
3.3188-3.43750.22051720.188715461718100
3.4375-3.57510.18761660.165114971663100
3.5751-3.73780.21261710.154415341705100
3.7378-3.93490.18471700.151415301700100
3.9349-4.18140.19751700.133115261696100
4.1814-4.50420.15721690.130115261695100
4.5042-4.95750.16391710.130315321703100
4.9575-5.67470.16881720.157615441716100
5.6747-7.1490.21441720.179515621734100
7.149-87.0110.21321810.164616231804100
Refinement TLS params.Method: refined / Origin x: 155.1619 Å / Origin y: 172.4373 Å / Origin z: 275.4977 Å
111213212223313233
T0.2522 Å2-0.0164 Å2-0.0254 Å2-0.2198 Å20.0131 Å2--0.2593 Å2
L0.2052 °2-0.1068 °2-0.215 °2-0.4731 °20.4445 °2--0.8654 °2
S-0.015 Å °0.0302 Å °-0.0037 Å °-0.0754 Å °0.0091 Å °0.0731 Å °-0.0691 Å °0.039 Å °0.0077 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 527
2X-RAY DIFFRACTION1allB1 - 522
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 79
5X-RAY DIFFRACTION1allE1 - 16
6X-RAY DIFFRACTION1allF1

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