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- PDB-4o26: Crystal structure of the TRBD domain of TERT and the CR4/5 of TR -

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Basic information

Entry
Database: PDB / ID: 4o26
TitleCrystal structure of the TRBD domain of TERT and the CR4/5 of TR
Components
  • Telomerase TR
  • Telomerase reverse transcriptase
KeywordsRNA BINDING PROTEIN/RNA / telomerase / telomerase RNA / protein-RNA interaction / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


DNA strand elongation / telomerase catalytic core complex / telomerase activity / telomerase RNA binding / telomeric DNA binding / telomere maintenance via telomerase / RNA-directed DNA polymerase / chromosome, telomeric region / metal ion binding
Similarity search - Function
Topoisomerase I; Chain A, domain 4 - #70 / : / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Topoisomerase I; Chain A, domain 4 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) ...Topoisomerase I; Chain A, domain 4 - #70 / : / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / Topoisomerase I; Chain A, domain 4 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Telomerase reverse transcriptase
Similarity search - Component
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsHuang, J. / Wu, J. / Lei, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural basis for protein-RNA recognition in telomerase.
Authors: Huang, J. / Brown, A.F. / Wu, J. / Xue, J. / Bley, C.J. / Rand, D.P. / Wu, L. / Zhang, R. / Chen, J.J. / Lei, M.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase reverse transcriptase
B: Telomerase reverse transcriptase
E: Telomerase TR
F: Telomerase TR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,84416
Polymers92,6924
Non-polymers1,15312
Water55831
1
A: Telomerase reverse transcriptase
E: Telomerase TR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,11410
Polymers46,3462
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-125 kcal/mol
Surface area21550 Å2
MethodPISA
2
B: Telomerase reverse transcriptase
F: Telomerase TR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7306
Polymers46,3462
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-66 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.092, 118.092, 358.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-711-

HOH

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Components

#1: Protein Telomerase reverse transcriptase / TERT


Mass: 29989.141 Da / Num. of mol.: 2 / Fragment: TRBD (UNP residues 318-572)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: TERT / Production host: Escherichia coli (E. coli) / Strain (production host): ScarabXpress T7lac / References: UniProt: Q1PS67
#2: RNA chain Telomerase TR


Mass: 16356.654 Da / Num. of mol.: 2 / Fragment: CR4/5 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Oryzias latipes (Japanese medaka)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate, pH 4.5, 1 M ammonium sulfate, 0.3 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 30608 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.9 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.118.40.56829981.021100
3.11-3.238.50.4129461.0951100
3.23-3.388.40.28730101.1711100
3.38-3.568.40.20529951.4631100
3.56-3.788.30.15530101.7881100
3.78-4.078.30.11630342.0971100
4.07-4.488.30.08630472.2821100
4.48-5.138.10.07830822.673199.9
5.13-6.467.90.07131282.7031100
6.46-1007.20.04933582.781198.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
REFMACrefinement
PDB_EXTRACT3.14data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.001→41.971 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 1536 5.03 %
Rwork0.2209 --
obs0.2229 30523 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 337.82 Å2 / Biso mean: 101.1978 Å2 / Biso min: 25.83 Å2
Refinement stepCycle: LAST / Resolution: 3.001→41.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 2000 60 31 5940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066219
X-RAY DIFFRACTIONf_angle_d1.0188826
X-RAY DIFFRACTIONf_chiral_restr0.0671023
X-RAY DIFFRACTIONf_plane_restr0.005764
X-RAY DIFFRACTIONf_dihedral_angle_d21.012603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.001-3.09830.2961130.252725832696100
3.0983-3.2090.30021590.252225312690100
3.209-3.33750.25471330.215225812714100
3.3375-3.48930.27581420.210625912733100
3.4893-3.67310.25731480.199325812729100
3.6731-3.90310.23771560.194325822738100
3.9031-4.20420.22931460.1826252771100
4.2042-4.62680.20341260.177226242750100
4.6268-5.29520.22911180.210826822800100
5.2952-6.66710.3361360.2727252861100
6.6671-41.97480.27951590.24952882304199
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)
10.235-0.2607-0.05790.28710.14130.1440.08810.0885-0.0525-0.1242-0.1015-0.05-0.09-0.0327-0.01650.15860.7635-0.0995-0.2370.00670.282813.08666.366345.3591
20.25230.1952-0.12890.5933-0.14940.4334-0.0741-0.0499-0.0898-0.14380.26090.112-0.0556-0.33160.00660.45290.063-0.02580.34030.01910.400316.556231.839730.0152
30.18390.12720.01010.1047-0.00880.3242-0.05820.21790.2368-0.06450.1432-0.0658-0.3118-0.3015-0.02780.85250.349-0.40430.7703-0.1990.9446-16.357967.319428.3552
40.0569-0.07180.02530.05-0.01730.0818-0.06860.2064-0.0997-0.361-0.1389-0.15430.00320.4547-01.62870.12380.12671.2883-0.28351.461138.352518.24414.3657
50.2259-0.02750.11710.013-0.0410.27550.08890.00290.13350.21550.2007-0.08610.16090.12410.13260.65620.190.10120.4502-0.0970.512514.559458.713851.0899
60.0029-0.0415-0.01460.03460.03140.0039-0.01250.0021-0.0342-0.0636-0.0111-0.03530.01220.0162-0.01680.30510.11260.04530.2569-0.02390.152314.218855.943245.1073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 316 through 572)A316 - 572
2X-RAY DIFFRACTION2chain 'B' and (resid 317 through 564)B317 - 564
3X-RAY DIFFRACTION3chain 'E' and (resid 170 through 220)E170 - 220
4X-RAY DIFFRACTION4chain 'F' and (resid 170 through 220)F170 - 220
5X-RAY DIFFRACTION5chain 'A' and (resid 601 through 608) or chain 'B' and (resid 601 through 604)A601 - 608
6X-RAY DIFFRACTION5chain 'A' and (resid 601 through 608) or chain 'B' and (resid 601 through 604)B601 - 604
7X-RAY DIFFRACTION6chain 'A' and (resid 701 through 721) or chain 'B' and (resid 701 through 708) or chain 'E' and (resid 301 through 302)A701 - 721
8X-RAY DIFFRACTION6chain 'A' and (resid 701 through 721) or chain 'B' and (resid 701 through 708) or chain 'E' and (resid 301 through 302)B701 - 708
9X-RAY DIFFRACTION6chain 'A' and (resid 701 through 721) or chain 'B' and (resid 701 through 708) or chain 'E' and (resid 301 through 302)E301 - 302

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