[English] 日本語
Yorodumi
- PDB-6ieh: Crystal structures of the hMTR4-NRDE2 complex -

+
Open data


ID or keywords:

Loading...

-
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


negative regulation of RNA catabolic process / snRNA catabolic process / TRAMP complex / positive regulation of RNA export from nucleus / regulatory ncRNA-mediated heterochromatin formation / mRNA stabilization / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / catalytic step 2 spliceosome ...negative regulation of RNA catabolic process / snRNA catabolic process / TRAMP complex / positive regulation of RNA export from nucleus / regulatory ncRNA-mediated heterochromatin formation / mRNA stabilization / 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 / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / mRNA splicing, via spliceosome / mRNA processing / rRNA processing / mitotic cell cycle / RNA helicase activity / nuclear speck / RNA helicase / 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 / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT ...siRNA-mediated silencing protein NRDE-2 / NRDE-2, necessary for RNA interference / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more