[English] 日本語
Yorodumi
- PDB-5lsw: A CAF40-binding motif facilitates recruitment of the CCR4-NOT com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lsw
TitleA CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin
Components
  • Cell differentiation protein RCD1 homologCellular differentiation
  • LD12033p
KeywordsGENE REGULATION / DEADENYLATION / CCR4-NOT / TRANSLATIONAL REPRESSION / translation
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain ...CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / sex differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / RNA stem-loop binding / regulation of mRNA stability / nuclear receptor coactivator activity / P-body / RING-type E3 ubiquitin transferase / kinase binding / cytokine-mediated signaling pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytoplasmic stress granule / protein polyubiquitination / ubiquitin protein ligase activity / double-stranded RNA binding / positive regulation of peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / negative regulation of translation / protein domain specific binding / mRNA binding / protein homodimerization activity / protein-containing complex / RNA binding / zinc ion binding / membrane / nucleus / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / Roquin II / Roquin II domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / Roquin II / Roquin II domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 9 / RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSgromo, A. / Raisch, T. / Bawankar, P. / Bhandari, D. / Chen, Y. / Kuzuoglu-Ozturk, D. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Nat Commun / Year: 2017
Title: A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted by Drosophila Roquin.
Authors: Sgromo, A. / Raisch, T. / Bawankar, P. / Bhandari, D. / Chen, Y. / Kuzuoglu-Ozturk, D. / Weichenrieder, O. / Izaurralde, E.
History
DepositionSep 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cell differentiation protein RCD1 homolog
B: LD12033p
C: Cell differentiation protein RCD1 homolog
D: LD12033p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32810
Polymers66,7004
Non-polymers6296
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-44 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.930, 103.690, 60.830
Angle α, β, γ (deg.)90.00, 113.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cell differentiation protein RCD1 homolog / Cellular differentiation / Rcd-1 / CCR4-NOT transcription complex subunit 9


Mass: 31072.189 Da / Num. of mol.: 2 / Fragment: UNP residues 19-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RQCD1, CNOT9, RCD1 / Plasmid: PETMCN(PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600
#2: Protein/peptide LD12033p / Roquin / isoform A / isoform B / isoform C


Mass: 2277.593 Da / Num. of mol.: 2 / Fragment: UNP residues 790-810 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VV48
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium Acetate pH 5.0 17.5 % (w/v) PEG 4000 0.1 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2014 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.15→46.8 Å / Num. obs: 34975 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.999 / Rsym value: 0.048 / Net I/σ(I): 13.6
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.519 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV2, CHAIN A

2fv2


Resolution: 2.15→46.769 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2262 1851 5.29 %
Rwork0.184 --
obs0.1861 34964 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 36 191 4905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044794
X-RAY DIFFRACTIONf_angle_d0.5976508
X-RAY DIFFRACTIONf_dihedral_angle_d14.8422948
X-RAY DIFFRACTIONf_chiral_restr0.038772
X-RAY DIFFRACTIONf_plane_restr0.004818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1499-2.20810.29331570.26282495X-RAY DIFFRACTION99
2.2081-2.2730.24811830.22672520X-RAY DIFFRACTION99
2.273-2.34640.25911610.22162515X-RAY DIFFRACTION99
2.3464-2.43030.28071530.20342522X-RAY DIFFRACTION99
2.4303-2.52760.24931510.20462557X-RAY DIFFRACTION99
2.5276-2.64260.25811350.20122550X-RAY DIFFRACTION99
2.6426-2.78190.23641360.19842541X-RAY DIFFRACTION99
2.7819-2.95620.25611310.20332570X-RAY DIFFRACTION99
2.9562-3.18440.28341300.19912579X-RAY DIFFRACTION99
3.1844-3.50470.23171220.18832557X-RAY DIFFRACTION99
3.5047-4.01160.18171280.16612566X-RAY DIFFRACTION98
4.0116-5.05330.19851300.15632549X-RAY DIFFRACTION98
5.0533-46.78020.20031340.17052592X-RAY DIFFRACTION98
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)
13.76010.0165-0.55683.2378-0.67241.6384-0.10860.09090.1403-0.06190.0952-0.03870.1378-0.08550.00450.2646-0.0023-0.03710.2694-0.00530.1901-15.38882.508-8.3394
23.92112.69040.54782.18610.76610.4619-0.28470.90890.5784-1.14210.08271.0005-0.03-0.45650.02450.65-0.0793-0.09780.5976-0.0090.2565-18.33061.0586-21.9803
32.89150.4710.48672.23890.66310.969-0.10820.0411-0.03590.06160.07510.0931-0.02540.0421-0.00280.2614-0.00180.01770.27770.02080.2249-13.034942.7008-9.0895
40.50690.35370.12141.1252-0.08340.4055-0.33620.6363-0.1849-0.94440.1978-1.42070.1120.51850.00550.5389-0.09180.07820.58610.02810.4479-10.118843.4578-22.8989
51.5721-1.8334-0.13892.40340.39831.47850.07310.59591.4475-1.133-0.3229-2.4281-0.60830.6818-0.38410.74760.04770.47280.7450.52051.26071.166720.8492-24.745
62.6505-1.4465-0.37471.2071-0.30623.13110.0080.2454-1.5487-1.0251-0.41272.10361.1713-0.1173-0.70120.6102-0.0904-0.30160.3038-0.28990.9358-29.85123.535-24.3633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 13 through 201)
2X-RAY DIFFRACTION2(chain 'B' and resid 790 through 810)
3X-RAY DIFFRACTION3(chain 'C' and resid 13 through 201)
4X-RAY DIFFRACTION4(chain 'D' and resid 790 through 810)
5X-RAY DIFFRACTION5(chain 'A' and resid 202 through 285)
6X-RAY DIFFRACTION6(chain 'C' and resid 202 through 285)

+
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