[English] 日本語
Yorodumi
- PDB-7voi: Structure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7voi
TitleStructure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 6-like
  • CCR4-NOT transcription complex subunit 7
KeywordsHYDROLASE / CCR4-NOT complex mRNA degradation / RNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / RNA exonuclease activity / armadillo repeat domain binding / CCR4-NOT core complex / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / CCR4-NOT complex ...regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / RNA exonuclease activity / armadillo repeat domain binding / CCR4-NOT core complex / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / regulation of stem cell population maintenance / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body assembly / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / negative regulation of type I interferon-mediated signaling pathway / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / intracellular membraneless organelle / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of viral genome replication / nuclear estrogen receptor binding / P-body / mRNA processing / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / defense response to virus / molecular adaptor activity / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / nuclear body / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 6-like / CCR4-NOT transcription complex subunit 7/8/Pop2 / : / Ribonuclease CAF1 / CAF1 family ribonuclease / : / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-NOT transcription complex subunit 1, NOT1_connector / : / CCR4-Not complex component, Not1, C-terminal ...CCR4-NOT transcription complex subunit 6-like / CCR4-NOT transcription complex subunit 7/8/Pop2 / : / Ribonuclease CAF1 / CAF1 family ribonuclease / : / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-NOT transcription complex subunit 1, NOT1_connector / : / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily / CCR4-NOT transcription complex subunit 1 / CCR4-Not complex component, Not1 / CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 / CCR4-NOT transcription complex subunit 1 CAF1-binding domain / CCR4-NOT transcription complex subunit 1 TTP binding domain / CCR4-NOT transcription complex subunit 1 HEAT repeat / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 6-like / CCR4-NOT transcription complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.38 Å
AuthorsBartlam, M. / Zhang, Q.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053
National Natural Science Foundation of China (NSFC)31800627
CitationJournal: Protein Sci. / Year: 2022
Title: Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements.
Authors: Zhang, Q. / Pavanello, L. / Potapov, A. / Bartlam, M. / Winkler, G.S.
History
DepositionOct 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: CCR4-NOT transcription complex subunit 7
A: CCR4-NOT transcription complex subunit 1
C: CCR4-NOT transcription complex subunit 6-like


Theoretical massNumber of molelcules
Total (without water)122,4813
Polymers122,4813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.989, 110.989, 242.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein CCR4-NOT transcription complex subunit 7 / BTG1-binding factor 1 / CCR4-associated factor 1 / CAF-1 / Caf1a


Mass: 32776.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT7, CAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UIV1, poly(A)-specific ribonuclease
#2: Protein CCR4-NOT transcription complex subunit 1 / CCR4-associated factor 1 / Negative regulator of transcription subunit 1 homolog / NOT1H / hNOT1


Mass: 26628.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT1, CDC39, KIAA1007, NOT1, AD-005 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5YKK6
#3: Protein CCR4-NOT transcription complex subunit 6-like / Carbon catabolite repressor protein 4 homolog B


Mass: 63076.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 8% PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 4.38→50 Å / Num. obs: 10302 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 161.92 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 27.3
Reflection shellResolution: 4.38→4.48 Å / Num. unique obs: 493 / CC1/2: 0.93 / Rpim(I) all: 0.177

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B8C, 4GMJ

4b8c

4gmj


Resolution: 4.38→38.74 Å / SU ML: 0.5167 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.5109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3239 1009 9.99 %
Rwork0.2625 9094 -
obs0.2687 10103 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 198.04 Å2
Refinement stepCycle: LAST / Resolution: 4.38→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 0 0 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565564
X-RAY DIFFRACTIONf_angle_d0.96057529
X-RAY DIFFRACTIONf_chiral_restr0.065839
X-RAY DIFFRACTIONf_plane_restr0.0071964
X-RAY DIFFRACTIONf_dihedral_angle_d9.3148719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.38-4.610.31391320.26771213X-RAY DIFFRACTION93.21
4.61-4.90.33131410.24131272X-RAY DIFFRACTION98.88
4.9-5.280.29111440.23681293X-RAY DIFFRACTION99.24
5.28-5.810.29971450.27131299X-RAY DIFFRACTION98.7
5.81-6.640.33881440.27391289X-RAY DIFFRACTION98.49
6.65-8.360.30091480.27081338X-RAY DIFFRACTION99.13
8.36-38.740.34391550.26381390X-RAY DIFFRACTION96.68
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)
15.256505677981.07605876922-0.6487470071230.430999478934-0.54714167442.316916785910.3080302330350.07422607683330.565092313337-0.120358200781-0.1907302948840.0390091537840.02451242116010.1613036936120.0002229250661241.387441730.0003175783835850.008784658029811.60371453692-0.03897981419941.51243679637141.9753445739.58200991436275.4446203
21.336811098561.19738887506-0.6211824869344.876285935260.3695852170270.490368802180.07551782732640.0856102164498-0.2197606155110.1910350734820.0984409107542-0.6789394311710.209402486661-0.2140524728940.0002893920537881.313852967340.0595376307422-0.1974031477891.628638070430.2271177593791.5549473815159.724840102-7.67994181495298.462080266
35.096192042871.25498101564-2.577007136761.0978845828-1.516730437263.716837162140.1631983680330.05084657478990.3854390240540.644338841475-0.0797859744240.224883741226-0.832955355607-0.0320905916344-0.0009029608681531.9622813530.0508406860463-0.2287751994131.50014817839-0.004753196487552.13222681622109.61777055120.0357029401304.171233738
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 10 through 280)BA10 - 2801 - 264
22(chain 'A' and resid 1089 through 1317)AB1089 - 13171 - 229
33(chain 'C' and resid 37 through 526)CC37 - 5261 - 180

+
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