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- PDB-4c0d: Structure of the NOT module of the human CCR4-NOT complex (CNOT1-... -

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Basic information

Entry
Database: PDB / ID: 4c0d
TitleStructure of the NOT module of the human CCR4-NOT complex (CNOT1-CNOT2-CNOT3)
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 / HYDROLASE / TRANSCRIPTION
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: 3.2 Å
AuthorsRaisch, T. / Jonas, S. / Boland, A. / Chen, Y. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure and Assembly of the not Module of the Human Ccr4-not Complex
Authors: Boland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Kuzuoglu-Ozturk, D. / Wohlbold, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionAug 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: 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 CHAIN B AND C ARE BIFURCATED. ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. THE SHEET STRUCTURES OF CHAIN B AND C ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS B AND C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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)136,2113
Polymers136,2113
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-82.2 kcal/mol
Surface area36930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.570, 165.920, 78.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 92672.805 Da / Num. of mol.: 1
Fragment: NOT1 SUPERFAMILY HOMOLOGY DOMAIN, RESIDUES 1565-2371
Source method: isolated from a genetically manipulated source
Details: SAMPLE WAS PROTEOLYSED PRIOR TO CRYSTALLIZATION. MOST OF THE MISSING RESIDUES (REMARK 465) ARE PROBABLY NOT IN THE CRYSTAL
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: 23313.465 Da / Num. of mol.: 1
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 344-540
Source method: isolated from a genetically manipulated source
Details: SAMPLE WAS PROTEOLYSED PRIOR TO CRYSTALLIZATION. MOST OF THE MISSING RESIDUES (REMARK 465) ARE PROBABLY NOT IN THE CRYSTAL
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: 20224.588 Da / Num. of mol.: 1
Fragment: NOT ANCHOR REGION AND NOT-BOX DOMAIN, RESIDUES 607-753
Source method: isolated from a genetically manipulated source
Details: SAMPLE WAS PROTEOLYSED PRIOR TO CRYSTALLIZATION. MOST OF THE MISSING RESIDUES (REMARK 465) ARE PROBABLY NOT IN THE CRYSTAL
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, THE FIVE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. MISSING N- AND C-TERMINI DUE ...CHAIN A, THE FIVE N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. MISSING N- AND C-TERMINI DUE TO LIMITED PROTEOLYSIS PRIOR TO CRYSTALLIZATION. CHAIN B, THE FOUR N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG. MISSING N-TERMINUS DUE TO LIMITED PROTEOLYSIS PRIOR TO CRYSTALLIZATION. CHAIN C, THE FIRST 19 RESIDUES ARE AN EXPRESSION TAG. MISSING N- AND C-TERMINI DUE TO LIMITED PROTEOLYSIS PRIOR TO CRYSTALLIZATION.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.5 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES PH=6.5, 12% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2012 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3.2→48.5 Å / Num. obs: 20282 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 62.8 Å2 / Rsym value: 0.12 / Net I/σ(I): 10.1
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.56 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4C0E, 4C0F, 4C0G

4c0e

4c0f

4c0g


Resolution: 3.2→48.48 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 27.69 / Stereochemistry target values: ML
Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1870, 1874, 1890, 1927, 2086, 2141, 2146, 2147, 2149, 2150, 2151, 2155, 2185, 2204, 2205, 2331, 2350, 2351. ...Details: SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 1870, 1874, 1890, 1927, 2086, 2141, 2146, 2147, 2149, 2150, 2151, 2155, 2185, 2204, 2205, 2331, 2350, 2351. CHAIN B, RESIDUES 368, 428, 435. CHAIN C, RESIDUES 697, 701, 713, 718, 736, 737, 745, 748.
RfactorNum. reflection% reflection
Rfree0.2726 1035 5.1 %
Rwork0.2239 --
obs0.2262 20241 98.81 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.472 Å2 / ksol: 0.297 e/Å3
Displacement parametersBiso mean: 71.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.4448 Å20 Å20 Å2
2---28.7177 Å20 Å2
3---26.2728 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 0 0 6864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027071
X-RAY DIFFRACTIONf_angle_d0.5159638
X-RAY DIFFRACTIONf_dihedral_angle_d9.6552549
X-RAY DIFFRACTIONf_chiral_restr0.0381047
X-RAY DIFFRACTIONf_plane_restr0.0021243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1999-3.36860.35221530.30552708X-RAY DIFFRACTION99
3.3686-3.57960.32361410.27562699X-RAY DIFFRACTION99
3.5796-3.85590.30621380.2482679X-RAY DIFFRACTION98
3.8559-4.24370.31781610.21092704X-RAY DIFFRACTION99
4.2437-4.85730.23821620.18272745X-RAY DIFFRACTION99
4.8573-6.11770.23941500.21972761X-RAY DIFFRACTION99
6.1177-48.48520.22621300.20412910X-RAY DIFFRACTION98

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