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- PDB-11gz: TEP1 TIR/DUF4062 domain -

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Basic information

Entry
Database: PDB / ID: 11gz
TitleTEP1 TIR/DUF4062 domain
ComponentsTelomerase protein component 1
KeywordsHYDROLASE / NAD-ase / TIR domain / DUF4062 / TEP1 / RNA Vault
Function / homology
Function and homology information


telomerase activity / telomere maintenance via recombination / telomerase holoenzyme complex / telomerase RNA binding / nuclear matrix / p53 binding / chromosome, telomeric region / ribonucleoprotein complex / enzyme binding / RNA binding ...telomerase activity / telomere maintenance via recombination / telomerase holoenzyme complex / telomerase RNA binding / nuclear matrix / p53 binding / chromosome, telomeric region / ribonucleoprotein complex / enzyme binding / RNA binding / ATP binding / cytoplasm
Similarity search - Function
TEP1, N-terminal / Domain of unknown function DUF4062 / Domain of unknown function DUF5920 / : / : / : / TEP1 N-terminal domain / Domain of unknown function (DUF4062) / Domain of unknown function (DUF5920) / TEP-1 second beta-propeller ...TEP1, N-terminal / Domain of unknown function DUF4062 / Domain of unknown function DUF5920 / : / : / : / TEP1 N-terminal domain / Domain of unknown function (DUF4062) / Domain of unknown function (DUF5920) / TEP-1 second beta-propeller / TEP-1 C-terminal beta-propeller / TEP1 N-terminal repeat profile. / TROVE domain / TROVE domain / TROVE domain superfamily / TROVE domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / WD domain, G-beta repeat / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Telomerase protein component 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsOsinski, A. / Tomchick, D.R. / Tagliabracci, V.S.
Funding support United States, 5items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158265 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
Welch FoundationI-1911 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 United States
CitationJournal: Biorxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault
Authors: Osinski, A. / Mayro, B. / Lopez, V.A. / Schrad, J. / Choi, H. / Tomchick, D.R. / Pawlowski, K. / Forsberg, K. / Shahmoradian, S.H. / Tagliabracci, V.S.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase protein component 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6274
Polymers25,4071
Non-polymers2203
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.762, 132.762, 132.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Space group name HallP4acd2ab3
Components on special symmetry positions
IDModelComponents
11A-1319-

HOH

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Components

#1: Protein Telomerase protein component 1 / Telomerase-associated protein 1 / Telomerase protein 1 / p240 / p80 telomerase homolog


Mass: 25406.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEP1, TLP1, TP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q99973
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1:1 protein:reservoir solution 40 mg/mL protein with 2 mM Benzamide Adenine dinucleotide 14-19% PEG 3350, 0.2 M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.438→40.03 Å / Num. obs: 15064 / % possible obs: 97.07 % / Redundancy: 58.5 % / Biso Wilson estimate: 32.72 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.011 / Rrim(I) all: 0.086 / Χ2: 1.144 / Net I/σ(I): 9.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 30.5 % / Rmerge(I) obs: 2.617 / Num. unique obs: 759 / CC1/2: 0.504 / CC star: 0.819 / Rpim(I) all: 0.466 / Rrim(I) all: 2.66 / Χ2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
BUSTERrefinement
ISOLDEmodel building
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→40.03 Å / SU ML: 0.2515 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 1505 9.99 %RANDOM
Rwork0.2361 13553 --
obs0.2411 15058 97.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.41 Å2
Refinement stepCycle: LAST / Resolution: 2.44→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 13 137 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841847
X-RAY DIFFRACTIONf_angle_d0.72132496
X-RAY DIFFRACTIONf_chiral_restr0.0465256
X-RAY DIFFRACTIONf_plane_restr0.0085326
X-RAY DIFFRACTIONf_dihedral_angle_d18.6005689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.520.3443980.2909883X-RAY DIFFRACTION70.52
2.52-2.610.37621360.3021217X-RAY DIFFRACTION98.26
2.61-2.710.31921350.27171218X-RAY DIFFRACTION98.98
2.71-2.830.31861360.26611238X-RAY DIFFRACTION99.93
2.83-2.980.27131380.25211238X-RAY DIFFRACTION100
2.98-3.170.2971390.26411255X-RAY DIFFRACTION99.93
3.17-3.410.31451400.25881262X-RAY DIFFRACTION100
3.42-3.760.25041410.21481267X-RAY DIFFRACTION100
3.76-4.30.27361410.20011272X-RAY DIFFRACTION99.86
4.3-5.420.25351460.19481300X-RAY DIFFRACTION100
5.42-40.030.28781550.24511403X-RAY DIFFRACTION99.94
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)
11.389181461790.932178166858-0.2170871639740.839919890107-0.3567952825071.32115023351-0.00443957559874-0.06135657913050.1796651073720.0382768302652-0.04517820398160.0451559363032-0.4229902613380.094452707501-0.8162944702620.904835098768-0.384324271505-0.006548541083610.3770225211354.55971480468E-50.221181603637-41.816395877116.837810227615.8771650503
20.874764811551-0.3305291125680.1039537233270.9220859879750.6647116247390.953341593728-0.06998311775570.176468448078-0.042748616454-0.08034309868920.01284128997970.00548837934747-0.0583793430184-0.00176900594514-0.603158047010.557693109754-0.177417075145-0.01044259580540.124350456852-0.142862921047-0.136561891158-42.60437036455.2007479869515.8019240548
30.857244673981-0.119245009804-0.4918607366990.01733632160290.06807012069960.282474297162-0.2287328607470.429153426624-0.0685073052662-0.696205101297-0.108223046350.2225174502960.213442805519-0.4190331273910.2730835396171.00851057618-0.152989765456-0.2087501592930.349090415876-0.03438877035920.26508587354-46.232122535314.338102559215.7722101757
42.78978311625-3.412748751663.396125927564.22229433628-4.246998687994.362828524230.1038755325870.888061248073-0.3526305318310.462930786776-0.1627634198820.4945709839690.570813236116-0.3989549621250.04389584112912.06069023809-0.4641813593640.1865336659241.78422217131-0.02620629649260.831432784165-50.938724446113.3031907204-2.95954069739
51.799570794582.78823660685-0.3147308852446.36000183442-3.225092718283.727362025250.310270815512-0.429877861559-0.154653142980.397795586565-0.551326364997-1.29780272655-0.83231061856-0.5351120984550.1449724310741.70624676322-0.390568733137-0.1219103363531.459726335020.06067509731490.634852052146-42.000005657717.0288233204-2.72388778286
62.987389954281.76614061962-1.019008535182.73473660715-0.7882375386762.04385998932-0.8661976856621.01312093307-0.100559494079-1.313655624020.6407125131160.1796538200180.541058649911-0.278353663740.2562500828791.18856313527-0.527369686539-0.1159534908080.6660387980360.2080101632540.526362029221-38.267402512321.32357190728.67006089883
72.22171299315-0.846516236381-1.396445651442.371468001622.029913032121.97304523464-0.3568900747510.740058572639-0.288919527043-0.5274216726430.369169077039-0.359301107490.362374855754-0.2602533663460.09742187341010.605714671207-0.3128072134340.2160310853470.44873079517-0.07136968496020.22880403692-32.97898376999.7536788802912.0135173466
80.7576575843190.5602693037131.22451181081.18353864920.4699174450422.22589919638-0.156824418308-0.1344070220480.110046170127-0.3814383623430.20313100716-0.0789405922099-0.026011988454-0.169087870816-0.221744350290.94306046055-0.6703505034030.2319462425141.28700551807-0.3312714026130.543533541918-31.07007698175.63718305036-1.28280847184
97.14406206296-0.951513922944-6.031898250212.64980370309-0.7695856235656.3831238795-0.3548504597451.38894088797-0.322811178879-0.3718806995090.04898565447980.06854354476280.411038327896-0.9708718840420.0631909922971.87727234581-0.6610118533150.4074797482151.517725046660.00700187605790.699844455158-29.256130175423.5267148975-1.27444848521
102.466955549921.69504310384-1.363518810872.20065131102-1.727016474371.83645519392-0.3909650755410.547218076339-0.217509263875-0.610134363490.30088826521-0.1815227013250.263430449177-0.0765876686009-0.2360799168251.0552859418-0.6548638764570.2083155898730.8912637091770.04205503142570.498305964285-29.200247126516.50104027395.32431441351
110.002841550412460.000477149591897-0.001670956951580.001996649157240.0008313945610620.001961916217560.01353789491420.0131199015548-0.00649429477276-0.02365125636540.034599274857-0.01002625367710.02221435263390.0566969623153-0.0001325404218671.31802152576-0.381185307151-0.1267793726931.381188841950.1790427447761.41377388111-28.16572299225.776662057615.3194732496
120.047593978918-0.0509413358734-0.02072613349570.1226820776050.05145067418410.05880515310780.05792708597810.109766307905-0.02432447244410.0001462456315540.0154718324879-0.0416382556814-0.03863452002710.225506054913-0.004918472160910.53435352493-0.3076799629360.1428010511440.894393592481-0.2957457450860.329765148586-29.02948655938.4898175823415.013251425
130.07035148250930.002253886938280.02940161742990.00489109194418-0.003846282659960.0188420582847-0.00399425798073-0.00610394119081-0.01773103981120.00933716394750.023123073541-0.03998414871050.03522555833490.0352171555193-0.1403269737760.214830551630.0875093304325-0.01012949946370.444031181978-0.2096300930720.112196228108-34.0790177469-10.86685838822.84842355268
140.127530078585-0.0323785476147-0.1502671289620.008196764870220.03881698666030.1764344314450.007528579072210.01827975661140.00129563909852-0.04216097921980.00109086913094-0.0274880639058-0.001488621301980.075620627794-0.02419238994030.361661922356-0.1048159776590.1988898493580.483977861703-0.1822535153290.214105790552-33.050657286-5.05944806488-0.708429587698
150.1654641477790.0467574339307-0.09543663363410.0168296799648-0.02285054741250.0598775522472-0.004056824846550.0334565151695-0.00760372035065-0.0205612170515-0.0211799811584-0.02795872189430.0260718579680.0171312304626-0.001170028587680.587598231936-0.2255457438930.3493892757761.02580175569-0.10260268190.658274621831-23.90092810641.39390012975-4.92703012494
160.00294311484069-0.007597156833580.005670366593920.0279298463491-0.02083318024160.0156415358091-0.06947361714560.02272799039690.127670766896-0.02359520414970.00836380205236-0.0758385562225-0.0122138659906-0.000732188891181-0.05969338115870.94863079836-0.6693671497540.2886900885231.50237949448-0.477637566120.886781689584-20.05600611548.994851212987.20334691219
175.24653163678E-50.00202702693035-0.001187673003440.00289154975555-0.004779855267150.007220151747460.02557449192420.001970110561930.02314799423480.01492065393990.0302975847978-0.05508840043740.00247376882110.185620881925-0.05023055109560.377179403216-0.1004912905780.004830044444730.888889610057-0.2947520331370.365457388751-27.27177367833.3420454831816.3499309761
180.1781236328310.025140040257-0.159293709210.0992526299931-0.04790633100580.149863986432-0.0125908144117-0.00990969879799-0.00304821918970.228969150701-0.07305129471380.05844475820460.106909690355-0.0651205256575-0.5904968905040.4325630017280.05931290320790.05077775753480.426280044156-0.267503098473-0.033650563619-39.4280013007-4.7957056906112.0903707201
19-2.14339249734E-5-0.000235610680346-6.84148778612E-50.00184041727627-0.000133249900692.71480282171E-50.02263992738950.0247146629397-0.0120136576780.008138048877070.0600337660043-0.04218397133350.05526332008020.1395696785380.1406290121120.397756878123-0.1655085490220.04061897077350.248991560201-0.09996442021710.0773679444278-35.52301469529.3773700216324.8761341658
200.0931816511254-0.0820468764922-0.04244465144120.07635795577890.03161470283130.0296299746284-0.0214955643755-0.003391764514350.0383845597687-0.03713837524370.0580662529382-0.0600000641898-0.02166034905510.0603665478732-0.01701871006140.597369217183-0.223769976239-0.03580634573880.309340038055-0.1439499546010.272812559233-34.806492406419.093564548227.7668381192
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 894:907)894 - 9071 - 14
22(chain A and resid 908:930)908 - 93015 - 37
33(chain A and resid 931:945)931 - 94538 - 52
44(chain A and resid 946:950)946 - 95053 - 57
55(chain A and resid 951:957)951 - 95758 - 64
66(chain A and resid 958:967)958 - 96765 - 74
77(chain A and resid 968:974)968 - 97475 - 81
88(chain A and resid 975:979)975 - 97982 - 86
99(chain A and resid 980:1001)980 - 100187 - 108
1010(chain A and resid 1002:1014)1002 - 1014109 - 121
1111(chain A and resid 1015:1020)1015 - 1020122 - 127
1212(chain A and resid 1021:1032)1021 - 1032128 - 139
1313(chain A and resid 1033:1042)1033 - 1042140 - 149
1414(chain A and resid 1043:1048)1043 - 1048150 - 155
1515(chain A and resid 1049:1054)1049 - 1054156 - 161
1616(chain A and resid 1055:1068)1055 - 1068162 - 175
1717(chain A and resid 1069:1077)1069 - 1077176 - 184
1818(chain A and resid 1078:1098)1078 - 1098185 - 205
1919(chain A and resid 1099:1105)1099 - 1105206 - 212
2020(chain A and resid 1106:1113)1106 - 1113213 - 220

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