[English] 日本語
Yorodumi
- PDB-6s8s: Extended structure of the human DDX6 C-terminal domain in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s8s
TitleExtended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide
Components
  • Enhancer of mRNA-decapping protein 3
  • Probable ATP-dependent RNA helicase DDX6
KeywordsRNA BINDING PROTEIN / Translational control / mRNA decay / miRNA
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity ...deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / viral RNA genome packaging / P-body assembly / miRNA-mediated gene silencing by inhibition of translation / RISC complex / stem cell population maintenance / negative regulation of neuron differentiation / stress granule assembly / helicase activity / P-body / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / negative regulation of translation / RNA helicase activity / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF ...Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Scd6-like Sm domain / Lsm14-like, N-terminal / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / : / DEAD-box subfamily ATP-dependent helicases signature. / Sm domain profile. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable ATP-dependent RNA helicase DDX6 / Enhancer of mRNA-decapping protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPeter, D. / Valkov, E.
CitationJournal: Genes Dev. / Year: 2019
Title: Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression.
Authors: Peter, D. / Ruscica, V. / Bawankar, P. / Weber, R. / Helms, S. / Valkov, E. / Igreja, C. / Izaurralde, E.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DDX6
B: Enhancer of mRNA-decapping protein 3
C: Probable ATP-dependent RNA helicase DDX6
D: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,05118
Polymers55,0904
Non-polymers1,96114
Water4,648258
1
A: Probable ATP-dependent RNA helicase DDX6
B: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68410
Polymers27,5452
Non-polymers1,1398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-36 kcal/mol
Surface area11830 Å2
MethodPISA
2
C: Probable ATP-dependent RNA helicase DDX6
D: Enhancer of mRNA-decapping protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3688
Polymers27,5452
Non-polymers8236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-36 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.425, 47.878, 65.757
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-415-

HOH

-
Components

#1: Protein Probable ATP-dependent RNA helicase DDX6 / ATP-dependent RNA helicase p54 / DEAD box protein 6 / Oncogene RCK


Mass: 22475.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX6, HLR2, RCK / Production host: Escherichia coli (E. coli) / References: UniProt: P26196, RNA helicase
#2: Protein/peptide Enhancer of mRNA-decapping protein 3 / LSM16 homolog / YjeF N-terminal domain-containing protein 2 / hYjeF_N2 / YjeF domain-containing protein 1


Mass: 5069.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDC3, LSM16, YJDC, YJEFN2, PP844 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96F86
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M CAPS pH 10.5, 1.2 M NaH2PO4, 0.8 M K2HPO4, 0.2 M Li2SO4

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.21→25.31 Å / Num. obs: 25958 / % possible obs: 95.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 30.69 Å2 / Rsym value: 0.104 / Net I/σ(I): 9.6
Reflection shellResolution: 2.21→2.25 Å / Num. unique obs: 961 / Rsym value: 0.467

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WAX

2wax


Resolution: 2.21→25.31 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.193
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1314 5.06 %RANDOM
Rwork0.179 ---
obs0.181 25943 95.6 %-
Displacement parametersBiso max: 144.86 Å2 / Biso mean: 40.05 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-6.2111 Å20 Å22.9435 Å2
2---10.3715 Å20 Å2
3---4.1604 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.21→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 115 258 3775
Biso mean--69.38 41.2 -
Num. residues----415
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1288SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes603HARMONIC5
X-RAY DIFFRACTIONt_it3577HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4060SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3577HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4828HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.12
LS refinement shellResolution: 2.21→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2394 31 5.97 %
Rwork0.2338 488 -
all0.2341 519 -
obs--72.03 %
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)
11.60720.23430.27141.38770.22992.302-0.0106-0.07570.12450.0619-0.0233-0.1015-0.19070.13850.0339-0.0037-0.0118-0.0078-0.00750.0082-0.0203-29.4414.495524.2661
25.79860.59582.43233.23060.98824.1146-0.1317-0.57650.23790.2872-0.17770.18230.2011-0.49240.3095-0.1403-0.01470.0164-0.1045-0.0372-0.0541-41.85882.307221.9703
31.9234-0.34670.30581.1538-0.24261.48690.05690.0287-0.0418-0.0293-0.04960.01430.00050.0718-0.0074-0.0631-0.01630.0022-0.0015-0.022-0.0571-22.354314.0658-7.9614
44.87311.2374.86061.35541.42656.0656-0.19050.4087-0.1074-0.28160.2418-0.0889-0.34191.0469-0.0513-0.1146-0.01820.0407-0.00060.0272-0.054-5.57578.962-5.7014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A296 - 463
2X-RAY DIFFRACTION2{ B|* }B190 - 226
3X-RAY DIFFRACTION3{ C|* }C296 - 468
4X-RAY DIFFRACTION4{ D|* }D190 - 226

+
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