[English] 日本語
Yorodumi
- PDB-2way: Structure of the human DDX6 C-terminal domain in complex with an ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2way
TitleStructure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide
Components
  • ATP-DEPENDENT RNA HELICASE DDX6
  • ENHANCER OF MRNA-DECAPPING PROTEIN 3
KeywordsHYDROLASE / DEAD-BOX PROTEIN / NUCLEOTIDE-BINDING / P54 / RCK / MIRNA / P-BODIES / HELICASE / DECAPPING / RNA-BINDING / PROTO-ONCOGENE / PHOSPHOPROTEIN / CHROMOSOMAL REARRANGEMENT / ATP-DEPENDENT RNA HELICASE / CYTOPLASM / MRNA DECAY / ATP-BINDING
Function / homology
Function and homology information


concave side of sperm head / outer dense fiber / sperm annulus / deadenylation-independent decapping of nuclear-transcribed mRNA / spermatid differentiation / mRNA decay by 5' to 3' exoribonuclease / chromatoid body / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex ...concave side of sperm head / outer dense fiber / sperm annulus / deadenylation-independent decapping of nuclear-transcribed mRNA / spermatid differentiation / mRNA decay by 5' to 3' exoribonuclease / chromatoid body / viral RNA genome packaging / miRNA-mediated gene silencing by inhibition of translation / RISC complex / P-body assembly / stem cell population maintenance / negative regulation of neuron differentiation / heterochromatin / stress granule assembly / adherens junction / P-body / helicase activity / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / RNA helicase activity / negative regulation of translation / RNA helicase / cadherin binding / protein domain specific binding / mRNA binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Linker region of enhancer of mRNA-decapping protein 3 / Lsm16, N-terminal / Lsm14-like, N-terminal / Scd6-like Sm domain / 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 / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 2.3 Å
AuthorsTritschler, F. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural Basis for the Mutually Exclusive Anchoring of P Body Components Edc3 and Tral to the Dead Box Protein Ddx6/Me31B.
Authors: Tritschler, F. / Braun, J.E. / Eulalio, A. / Truffault, V. / Izaurralde, E. / Weichenrieder, O.
History
DepositionFeb 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-DEPENDENT RNA HELICASE DDX6
B: ENHANCER OF MRNA-DECAPPING PROTEIN 3
C: ATP-DEPENDENT RNA HELICASE DDX6
D: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4598
Polymers55,0904
Non-polymers3684
Water2,000111
1
A: ATP-DEPENDENT RNA HELICASE DDX6
B: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8215
Polymers27,5452
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-17.2 kcal/mol
Surface area11800 Å2
MethodPQS
2
C: ATP-DEPENDENT RNA HELICASE DDX6
D: ENHANCER OF MRNA-DECAPPING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6373
Polymers27,5452
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-15.7 kcal/mol
Surface area12310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.920, 80.460, 110.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ATP-DEPENDENT RNA HELICASE DDX6 / HUMAN DDX6 / DEAD BOX PROTEIN 6 / ATP-DEPENDENT RNA HELICASE P54 / ONCOGENE RCK


Mass: 22475.650 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 296-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: P26196, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide ENHANCER OF MRNA-DECAPPING PROTEIN 3 / HUMAN EDC3 / LSM16 HOMOLOG / YJEF DOMAIN-CONTAINING PROTEIN 1 / YJEF N-TERMINAL DOMAIN-CONTAINING ...HUMAN EDC3 / LSM16 HOMOLOG / YJEF DOMAIN-CONTAINING PROTEIN 1 / YJEF N-TERMINAL DOMAIN-CONTAINING PROTEIN 2 / YJEF_N2 / HYJEF_N2


Mass: 5069.437 Da / Num. of mol.: 2 / Fragment: FDF PEPTIDE, RESIDUES 192-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: Q96F86
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 % / Description: NONE
Crystal growDetails: 0.04 M KH2PO4, 16% PEG 8000, 20% GLYCEROL

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111)MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.3→45.5 Å / Num. obs: 17392 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2M

1s2m


Resolution: 2.3→45.5 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R: 0.391 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES A 383-387, A 413-419, A 461-472, B 192-198, B 225-228, C 296, C 383-389, C 413-419, C 463-472, D 192-195, D 226--228 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.275 944 5.1 %RANDOM
Rwork0.21 ---
obs0.214 17392 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.72 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 0 24 111 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9554072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70524.25160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56915531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.691520
X-RAY DIFFRACTIONr_chiral_restr0.1130.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.51791
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76122898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.66531233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2334.51174
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 81 -
Rwork0.222 1278 -
obs--98.12 %

+
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