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- PDB-9e70: Human XRN1 with Adenosine-3',5'-Bisphosphate (pAp) Bound -

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Basic information

Entry
Database: PDB / ID: 9.0E+70
TitleHuman XRN1 with Adenosine-3',5'-Bisphosphate (pAp) Bound
Components5'-3' exoribonuclease 1
KeywordsHYDROLASE / Exonuclease / XRN1 / pAp / Inhibitor
Function / homology
Function and homology information


cellular response to puromycin / cellular response to cycloheximide / mRNA decay by 5' to 3' exoribonuclease / 5'-3' RNA exonuclease activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / nuclear mRNA surveillance / G-quadruplex DNA binding / rRNA catabolic process ...cellular response to puromycin / cellular response to cycloheximide / mRNA decay by 5' to 3' exoribonuclease / 5'-3' RNA exonuclease activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / histone mRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / nuclear mRNA surveillance / G-quadruplex DNA binding / rRNA catabolic process / telomerase RNA binding / negative regulation of telomere maintenance via telomerase / response to testosterone / nuclear-transcribed mRNA catabolic process / P-body / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / negative regulation of translation / neuronal cell body / dendrite / RNA binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
5'-3' exoribonuclease 1 / Xrn1, D1 domain / Exoribonuclease Xrn1, D2/D3 domain / 5'-3' exoribonuclease 1, SH3-like domain / : / : / Xrn1 SH3-like domain / Exoribonuclease Xrn1 D1 domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, N-terminal ...5'-3' exoribonuclease 1 / Xrn1, D1 domain / Exoribonuclease Xrn1, D2/D3 domain / 5'-3' exoribonuclease 1, SH3-like domain / : / : / Xrn1 SH3-like domain / Exoribonuclease Xrn1 D1 domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, N-terminal / 5'-3' exoribonuclease / Xrn1, helical domain / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / 5'-3' exoribonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLockbaum, G.J. / Lynes, M.M. / Sickmier, E.A. / Grigoriu, S. / Boriack-Sjodin, P.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Characterization of exoribonuclease XRN1 as a cancer target and identification of adenosine-3',5'-bisphosphate as a potent enzyme inhibitor.
Authors: Lockbaum, G.J. / Lynes, M.M. / Shen, S.A. / Liu, J. / Holt, N. / Nayak, S.P. / Knockenhauer, K.E. / Yao, S. / Sickmier, E.A. / Raman, A. / Wu, J. / Case, A. / Shehaj, L. / Buker, S.M. / ...Authors: Lockbaum, G.J. / Lynes, M.M. / Shen, S.A. / Liu, J. / Holt, N. / Nayak, S.P. / Knockenhauer, K.E. / Yao, S. / Sickmier, E.A. / Raman, A. / Wu, J. / Case, A. / Shehaj, L. / Buker, S.M. / Grigoriu, S. / Ribich, S. / Blakemore, S.J. / Sparling, B.A. / Duncan, K.W. / Copeland, R.A. / Silver, S.J. / Boriack-Sjodin, P.A.
History
DepositionOct 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-3' exoribonuclease 1
B: 5'-3' exoribonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,81423
Polymers156,2032
Non-polymers1,61021
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.91, 63.97, 363.15
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-3' exoribonuclease 1 / Strand-exchange protein 1 homolog


Mass: 78101.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRN1, SEP1 / Cell (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: Q8IZH2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Non-polymers , 6 types, 744 molecules

#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2 M Potassium fluoride, pH 7.3, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.051 Å / Num. obs: 84285 / % possible obs: 99.98 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5788 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
PHASERphasing
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.051 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.088 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.173 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2274 4332 5.14 %
Rwork0.1866 79953 -
all0.189 --
obs-84285 99.983 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å2-0 Å2
2---0.013 Å20 Å2
3---0.015 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9252 0 101 723 10076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129744
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.84813179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54751124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.197560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.366101664
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.57410499
X-RAY DIFFRACTIONr_chiral_restr0.1270.21373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027511
X-RAY DIFFRACTIONr_nbd_refined0.2230.24509
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2696
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.235
X-RAY DIFFRACTIONr_mcbond_it4.044.1714433
X-RAY DIFFRACTIONr_mcangle_it5.7047.4575533
X-RAY DIFFRACTIONr_scbond_it5.5454.715311
X-RAY DIFFRACTIONr_scangle_it8.2368.3947631
X-RAY DIFFRACTIONr_lrange_it10.63745.83915167
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1540.2943350.25957880.2661230.9380.9541000.229
2.154-2.2130.2972970.23656730.23959700.9390.9611000.205
2.213-2.2770.2752940.22255240.22458180.9460.9661000.189
2.277-2.3470.2512600.20953900.21156500.9580.971000.179
2.347-2.4240.2732800.20652060.20954860.9530.9711000.176
2.424-2.5090.2682420.21250630.21553050.9550.9711000.179
2.509-2.6030.2572760.19648560.19951330.9560.97499.98050.167
2.603-2.7090.2892410.20147150.20549560.9490.9731000.172
2.709-2.8290.2752530.20445120.20747650.9510.9731000.179
2.829-2.9670.2722280.19543190.19945470.9520.9751000.173
2.967-3.1270.2312070.18741490.18943560.9630.9771000.168
3.127-3.3160.2332330.18738950.18941280.9630.9781000.172
3.316-3.5430.2112120.18437180.18639310.9710.98199.97460.176
3.543-3.8260.2311790.17934530.18136320.9660.9831000.175
3.826-4.1880.1781660.15431830.15533490.9780.9861000.154
4.188-4.6780.1941650.1529040.15230690.9770.9861000.154
4.678-5.3930.1921420.14925620.15127040.9780.9861000.155
5.393-6.5840.221400.19222130.19423530.9760.9831000.197
6.584-9.2260.1971130.18317550.18418680.9790.9831000.192
9.226-48.0510.153690.19110750.18811450.9860.97399.91270.228

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