[English] 日本語
Yorodumi
- PDB-5fu6: NOT module of the human CCR4-NOT complex (Crystallization mutant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fu6
TitleNOT module of the human CCR4-NOT complex (Crystallization mutant)
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / TRANSCRIPTION / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / 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 / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription corepressor binding / nuclear estrogen receptor binding / P-body / transcription coregulator activity / positive regulation of cold-induced thermogenesis / negative regulation of translation / molecular adaptor activity / protein domain specific binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / NOT2/NOT3/NOT5 C-terminal / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 ...CCR4-NOT complex subunit 2/3/5, C-terminal domain / CCR4-Not complex component, Not N-terminal domain / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / NOT2/NOT3/NOT5 C-terminal / 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 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 3 / CCR4-NOT transcription complex subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRaisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E.
CitationJournal: Embo J. / Year: 2016
Title: Distinct Modes of Recruitment of the Ccr4-not Complex by Drosophila and Vertebrate Nanos
Authors: Raisch, T. / Bhandari, D. / Sabath, K. / Helms, S. / Valkov, E. / Weichenrieder, O. / Izaurralde, E.
History
DepositionJan 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, E, F ARE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAINS B, C, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS B, C, E, F.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)205,6666
Polymers205,6666
Non-polymers00
Water0
1
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
E: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
F: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)102,8333
Polymers102,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-82.7 kcal/mol
Surface area37850 Å2
MethodPISA
2
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3


Theoretical massNumber of molelcules
Total (without water)102,8333
Polymers102,8333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-81.5 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 135.320, 101.330
Angle α, β, γ (deg.)90.00, 107.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1 / CNOT1


Mass: 61620.102 Da / Num. of mol.: 2
Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1833-2361
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A5YKK6
#2: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 / CCR4-ASSOCIATED FACTOR 2 / CNOT2


Mass: 22945.076 Da / Num. of mol.: 2
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 350-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9NZN8
#3: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 / CCR4-ASSOCIATED FACTOR 3 / LEUKOCYTE RECEPTOR CLUSTER MEMBER 2 / CNOT3


Mass: 18267.590 Da / Num. of mol.: 2
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 607-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN(PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O75175
Sequence detailsCHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, E. THE SIX N- ...CHAIN A, D. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN B, E. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. CHAIN C, F. THE SIX N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CITRATE PH 5.5, 10 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2015 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99982 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 43109 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.26 % / Biso Wilson estimate: 81.37 Å2 / Rsym value: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.27 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.63 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0D

4c0d


Resolution: 2.9→48.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.349
Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, ...Details: THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, 1833 TO 1841, 2005 TO 2009. CHAIN D, 1833 TO 1841, 2004 TO 2007. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN B, RESIDUE 489. CHAIN D, RESIDUE 2008. CHAIN E, RESIDUE 531.
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 2200 5.1 %RANDOM
Rwork0.1807 ---
obs0.1827 43108 99.57 %-
Displacement parametersBiso mean: 83.94 Å2
Baniso -1Baniso -2Baniso -3
1--6.0947 Å20 Å20.0698 Å2
2--14.7266 Å20 Å2
3----8.6319 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14109 0 0 0 14109
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114521HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.119731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4951SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes352HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2081HARMONIC5
X-RAY DIFFRACTIONt_it14521HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1844SEMIHARMONIC5
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_contact16800SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 183 5.74 %
Rwork0.2288 3003 -
all0.2298 3186 -
obs--99.78 %
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)
11.9631.1594-0.57232.5268-0.95870.81780.1194-0.1571-0.02360.2318-0.12160.1824-0.16040.0380.0022-0.1080.0311-0.0017-0.2046-0.1046-0.145636.403-12.502239.9704
21.5735-0.1846-0.46050.06380.84760.49060.04910.6646-0.1139-0.2959-0.26730.1728-0.1476-0.3050.2182-0.07930.1959-0.18420.0045-0.1255-0.00398.3263-17.532723.9057
32.9545-0.4985-1.53270.94540.98061.6260.13390.3768-0.3916-0.0004-0.50640.50780.023-0.47240.3725-0.23880.002-0.0244-0.161-0.18330.10441.2283-22.872441.7912
41.6368-0.08061.13912.8728-1.84172.4581-0.02850.1646-0.0424-0.4264-0.1128-0.10240.24230.30450.1413-0.12730.06370.0657-0.312-0.0669-0.256913.9197-52.705111.0777
51.2048-0.46471.07190.02540.22511.53540.0028-0.422-0.09470.104-0.0030.2176-0.1089-0.49310.0002-0.0713-0.06060.0557-0.0512-0.0312-0.0186-18.6157-47.2316107.4814
60.6644-0.20130.15910.58480.6731.54150.04460.00830.196-0.198-0.27840.22-0.1564-0.48530.2338-0.04370.0419-0.1233-0.134-0.0002-0.022-13.8287-42.103888.9946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F

+
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