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- PDB-2y35: Crystal structure of Xrn1-substrate complex -

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Basic information

Entry
Database: PDB / ID: 2y35
TitleCrystal structure of Xrn1-substrate complex
Components
  • DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
  • LD22664P
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / RNA DEGRADATION / EXONUCLEASE 5'-3' / RNA INTERFERENCE
Function / homology
Function and homology information


Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / imaginal disc fusion, thorax closure / positive regulation of imaginal disc growth / RNA-mediated post-transcriptional gene silencing => GO:0035194 / regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / dorsal closure / imaginal disc-derived wing morphogenesis / 5'-3' exoribonuclease activity ...Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / imaginal disc fusion, thorax closure / positive regulation of imaginal disc growth / RNA-mediated post-transcriptional gene silencing => GO:0035194 / regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / dorsal closure / imaginal disc-derived wing morphogenesis / 5'-3' exoribonuclease activity / nuclear-transcribed mRNA catabolic process, non-stop decay / RNA-mediated post-transcriptional gene silencing / rRNA catabolic process / nuclear-transcribed mRNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mRNA catabolic process / P-body / wound healing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / spermatogenesis / negative regulation of gene expression / negative regulation of apoptotic process / RNA binding / nucleus / cytoplasm
Similarity search - Function
5-3 exonuclease XRN1 DCP1-binding motif / 5-3 exonuclease XRN1, DCP1-binding motif / Exoribonuclease Xrn1, D2/D3 domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, D1 domain / Xrn1 SH3-like domain / 5'-3' exoribonuclease 1, SH3-like domain / 5'-3' exoribonuclease 1 / Exoribonuclease Xrn1 D1 domain / 5'-3' exoribonuclease ...5-3 exonuclease XRN1 DCP1-binding motif / 5-3 exonuclease XRN1, DCP1-binding motif / Exoribonuclease Xrn1, D2/D3 domain / Exoribonuclease Xrn1 D2/D3 domain / Xrn1, D1 domain / Xrn1 SH3-like domain / 5'-3' exoribonuclease 1, SH3-like domain / 5'-3' exoribonuclease 1 / Exoribonuclease Xrn1 D1 domain / 5'-3' exoribonuclease / Xrn1, helical domain / Xrn1, N-terminal / XRN 5'-3' exonuclease N-terminus / Xrn1 helical domain
Similarity search - Domain/homology
DNA / DNA (> 10) / 5'-3' exoribonuclease 1 / 5'-3' exoribonuclease 1
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
SYTHETIC CONSTRUCT (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsJinek, M. / Coyle, S.M. / Doudna, J.A.
CitationJournal: Mol.Cell / Year: 2011
Title: Coupled 5' Nucleotide Recognition and Processivity in Xrn1-Mediated Mrna Decay.
Authors: Jinek, M. / Coyle, S.M. / Doudna, J.A.
History
DepositionDec 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LD22664P
B: DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,7213
Polymers135,6972
Non-polymers241
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.990, 149.990, 154.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein LD22664P / PACMAN / ISOFORM A / XRN1


Mass: 132395.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-1140 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PFASTBAC1 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9VWI1, UniProt: E1JJR3*PLUS, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: DNA chain DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'


Mass: 3301.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYTHETIC CONSTRUCT (unknown)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 207 TO ALA

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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: 3.22 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.2, 1% (V/V) PEG 300.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.016246
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.016246 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. obs: 29498 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 76.04 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.52 / % possible all: 95.7

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
autoSHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.2→74.995 Å / SU ML: 0.39 / σ(F): 2 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 1180 4 %
Rwork0.2246 --
obs0.2265 29498 99.1 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.1 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso mean: 79.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.8673 Å20 Å20 Å2
2---2.8673 Å20 Å2
3---5.7346 Å2
Refinement stepCycle: LAST / Resolution: 3.2→74.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8104 65 1 17 8187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118692
X-RAY DIFFRACTIONf_angle_d1.01711450
X-RAY DIFFRACTIONf_dihedral_angle_d16.9173002
X-RAY DIFFRACTIONf_chiral_restr0.0661287
X-RAY DIFFRACTIONf_plane_restr0.0051463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.3460.32871420.29363393X-RAY DIFFRACTION97
3.346-3.52240.3261460.27373516X-RAY DIFFRACTION100
3.5224-3.74310.33541460.26153502X-RAY DIFFRACTION100
3.7431-4.03210.25961470.22263516X-RAY DIFFRACTION100
4.0321-4.43780.2651470.19573533X-RAY DIFFRACTION100
4.4378-5.07990.23361480.17633543X-RAY DIFFRACTION99
5.0799-6.39960.24171490.2193579X-RAY DIFFRACTION99
6.3996-75.01560.26741550.23153736X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.16330.5232-0.71191.9343-0.26891.0429-0.02860.27490.0394-0.57010.00250.19860.1882-0.20550.01180.19810.11070.0024-0.1885-0.0075-0.106256.841212.201128.98
20.6339-0.8275-0.12942.45430.13422.51050.0265-0.12620.17020.03310.064-0.0192-0.1255-0.0460.00120.12220.01450.11970.0999-0.03390.193453.277135.437260.5939
30.25650.12320.02910.13980.17570.32710.236-0.23830.07270.3969-0.3332-0.165-0.52190.6051-0.00020.3288-0.27020.04830.4401-0.0860.781384.974853.039346.4821
41.4591-0.99330.08331.4125-0.82111.17790.11880.29650.0998-0.3612-0.3288-0.3569-0.0973-0.0521-0.01460.32260.08340.06280.04030.02330.108244.163554.902521.9932
50.79490.14790.80730.4360.1990.8255-0.1056-0.11180.2845-0.0891-0.14080.0335-0.18990.10250.00020.390.01040.13890.20480.06090.555165.293549.745738.2554
60.01920.00360.00260.0092-0.01250.02040.0036-0.4380.25830.4428-0.250.2373-0.001-0.40370.00181.43020.00840.16841.46370.21360.805351.149320.25123.8996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:632)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 633:799)
3X-RAY DIFFRACTION3(CHAIN A AND (RESID 802:850 OR RESID 1031:1045))
4X-RAY DIFFRACTION4(CHAIN A AND RESID 851:1026)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1046:1140)
6X-RAY DIFFRACTION6CHAIN B

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