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- PDB-6ieh: Crystal structures of the hMTR4-NRDE2 complex -

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Basic information

Entry
Database: PDB / ID: 6ieh
TitleCrystal structures of the hMTR4-NRDE2 complex
Components
  • Exosome RNA helicase MTR4
  • Protein NRDE2 homolog
KeywordsRNA BINDING PROTEIN / RNA helicase / MTR4 / NRDE2 / Complex
Function / homology
Function and homology information


regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / negative regulation of RNA catabolic process / snRNA catabolic process / TRAMP complex / positive regulation of RNA export from nucleus / regulatory ncRNA-mediated heterochromatin formation / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / catalytic step 2 spliceosome ...regulatory ncRNA-mediated post-transcriptional gene silencing => GO:0035194 / negative regulation of RNA catabolic process / snRNA catabolic process / TRAMP complex / positive regulation of RNA export from nucleus / regulatory ncRNA-mediated heterochromatin formation / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / rRNA processing / mRNA splicing, via spliceosome / mitotic cell cycle / RNA helicase activity / RNA helicase / nuclear speck / cell division / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
siRNA-mediated silencing protein NRDE-2 / NRDE-2, necessary for RNA interference / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT ...siRNA-mediated silencing protein NRDE-2 / NRDE-2, necessary for RNA interference / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Tetratricopeptide-like helical domain superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Exosome RNA helicase MTR4 / Nuclear exosome regulator NRDE2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.892 Å
AuthorsChen, J.Y. / Yun, C.H.
CitationJournal: Genes Dev. / Year: 2019
Title: NRDE2 negatively regulates exosome functions by inhibiting MTR4 recruitment and exosome interaction.
Authors: Wang, J. / Chen, J. / Wu, G. / Zhang, H. / Du, X. / Chen, S. / Zhang, L. / Wang, K. / Fan, J. / Gao, S. / Wu, X. / Zhang, S. / Kuai, B. / Zhao, P. / Chi, B. / Wang, L. / Li, G. / Wong, C.C.L. ...Authors: Wang, J. / Chen, J. / Wu, G. / Zhang, H. / Du, X. / Chen, S. / Zhang, L. / Wang, K. / Fan, J. / Gao, S. / Wu, X. / Zhang, S. / Kuai, B. / Zhao, P. / Chi, B. / Wang, L. / Li, G. / Wong, C.C.L. / Zhou, Y. / Li, J. / Yun, C. / Cheng, H.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Exosome RNA helicase MTR4
A: Protein NRDE2 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6184
Polymers123,0752
Non-polymers5432
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-45 kcal/mol
Surface area43180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.305, 113.728, 80.717
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Exosome RNA helicase MTR4 / ATP-dependent RNA helicase DOB1 / ATP-dependent RNA helicase SKIV2L2 / Superkiller viralicidic ...ATP-dependent RNA helicase DOB1 / ATP-dependent RNA helicase SKIV2L2 / Superkiller viralicidic activity 2-like 2 / TRAMP-like complex helicase


Mass: 111188.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P42285, RNA helicase
#2: Protein Protein NRDE2 homolog


Mass: 11886.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRDE2, C14orf102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H7Z3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 50 mM Glycine pH 9.0, 100 mM NaCl, 33% (w/v) polyethylene glycol 300 (PEG 300)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 29469 / % possible obs: 98.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.077 / Net I/σ(I): 10
Reflection shellResolution: 2.9→3.05 Å / Num. unique obs: 4141 / Rpim(I) all: 0.369

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U4C

4u4c


Resolution: 2.892→40.1 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1496 5.09 %
Rwork0.2355 --
obs0.2364 29379 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.892→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7583 0 32 32 7647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0367763
X-RAY DIFFRACTIONf_angle_d2.38210549
X-RAY DIFFRACTIONf_dihedral_angle_d24.4642771
X-RAY DIFFRACTIONf_chiral_restr0.2021228
X-RAY DIFFRACTIONf_plane_restr0.0141356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8917-2.9850.35681250.34282518X-RAY DIFFRACTION98
2.985-3.09170.36551410.33692520X-RAY DIFFRACTION98
3.0917-3.21540.32171480.31632515X-RAY DIFFRACTION99
3.2154-3.36170.29261380.27322506X-RAY DIFFRACTION99
3.3617-3.53880.27411410.24592521X-RAY DIFFRACTION99
3.5388-3.76040.26691280.24722545X-RAY DIFFRACTION99
3.7604-4.05050.23771300.21992564X-RAY DIFFRACTION99
4.0505-4.45760.21651400.19452546X-RAY DIFFRACTION99
4.4576-5.10150.20051320.1922552X-RAY DIFFRACTION99
5.1015-6.42310.25931340.23232571X-RAY DIFFRACTION99
6.4231-40.10350.20161390.20662525X-RAY DIFFRACTION96

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