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- PDB-4j8s: Crystal structure of human CNOT1 MIF4G domain in complex with a T... -

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Basic information

Entry
Database: PDB / ID: 4j8s
TitleCrystal structure of human CNOT1 MIF4G domain in complex with a TTP peptide
Components
  • CCR4-NOT transcription complex subunit 1
  • Tristetraprolin
KeywordsPROTEIN BINDING / MIF4G / protein-protein interaction / TTP / cytosol
Function / homology
Function and homology information


regulation of keratinocyte apoptotic process / negative regulation of polynucleotide adenylyltransferase activity / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / protein-RNA sequence-specific adaptor activity / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of intracellular mRNA localization / negative regulation of 3'-UTR-mediated mRNA stabilization / negative regulation of hematopoietic stem cell differentiation / positive regulation of cytoplasmic mRNA processing body assembly / negative regulation of erythrocyte differentiation ...regulation of keratinocyte apoptotic process / negative regulation of polynucleotide adenylyltransferase activity / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / protein-RNA sequence-specific adaptor activity / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of intracellular mRNA localization / negative regulation of 3'-UTR-mediated mRNA stabilization / negative regulation of hematopoietic stem cell differentiation / positive regulation of cytoplasmic mRNA processing body assembly / negative regulation of erythrocyte differentiation / positive regulation of miRNA-mediated gene silencing / regulation of keratinocyte proliferation / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of keratinocyte differentiation / 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 / negative regulation of intracellular estrogen receptor signaling pathway / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 3'-UTR-mediated mRNA destabilization / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of viral transcription / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / nuclear retinoic acid receptor binding / myeloid cell differentiation / regulation of tumor necrosis factor production / cellular response to granulocyte macrophage colony-stimulating factor stimulus / C-C chemokine binding / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RNA polymerase binding / peroxisomal membrane / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / cellular response to glucocorticoid stimulus / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 3'-UTR-mediated mRNA stabilization / negative regulation of interleukin-2 production / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / response to starvation / p38MAPK cascade / mRNA catabolic process / cellular response to fibroblast growth factor stimulus / hematopoietic stem cell differentiation / mRNA transport / positive regulation of fat cell differentiation / heat shock protein binding / 14-3-3 protein binding / regulation of mRNA stability / negative regulation of cytokine production involved in inflammatory response / cellular response to epidermal growth factor stimulus / nuclear estrogen receptor binding / P-body / response to wounding / negative regulation of inflammatory response / cytoplasmic stress granule / MAPK cascade / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / molecular adaptor activity / negative regulation of translation / protein domain specific binding / ribonucleoprotein complex / mRNA binding / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular space / RNA binding / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 1 TTP binding domain / RNA-binding protein ZFP36-like / : / : / 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 TTP binding domain / RNA-binding protein ZFP36-like / : / : / 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 / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / mRNA decay activator protein ZFP36
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / Sulfur SAD / Resolution: 1.55 Å
AuthorsFrank, F. / Fabian, M.R. / Rouya, C. / Siddiqui, N. / Lai, W.S. / Karetnikov, A. / Blackshear, P.J. / Sonenberg, N. / Nagar, B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for the recruitment of the human CCR4-NOT deadenylase complex by tristetraprolin.
Authors: Fabian, M.R. / Frank, F. / Rouya, C. / Siddiqui, N. / Lai, W.S. / Karetnikov, A. / Blackshear, P.J. / Nagar, B. / Sonenberg, N.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2May 25, 2016Group: Structure summary
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 1
B: Tristetraprolin


Theoretical massNumber of molelcules
Total (without water)25,7912
Polymers25,7912
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 85.060, 85.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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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


Mass: 24033.293 Da / Num. of mol.: 1 / Fragment: unp residues 800-1004
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD-005, CDC39, CNOT1, KIAA1007, NOT1 / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5YKK6
#2: Protein/peptide Tristetraprolin / TTP / G0/G1 switch regulatory protein 24 / Growth factor-inducible nuclear protein NUP475 / Protein ...TTP / G0/G1 switch regulatory protein 24 / Growth factor-inducible nuclear protein NUP475 / Protein TIS11A / TIS11 / Zinc finger protein 36 homolog / Zfp-36


Mass: 1758.054 Da / Num. of mol.: 1 / Fragment: unp residues 312-326 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P26651
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE CRYSTALLIZED SEQUENCE CORRESPONDS TO ISOFORM 2 OF CNOT1

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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: 1.99 Å3/Da / Density % sol: 38.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 5.5, and 25 % PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 21, 2012
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30.07 Å / Num. all: 30045 / Num. obs: 29686 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Rsym value: 0.065 / Net I/σ(I): 28.8
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.45 / % possible all: 90.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: dev_828)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Sulfur SAD / Resolution: 1.55→30.07 Å / SU ML: 0.28 / σ(F): 1.33 / Phase error: 18.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 1507 5.08 %
Rwork0.1665 --
obs0.1676 29684 98.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.063 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 0 237 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121685
X-RAY DIFFRACTIONf_angle_d1.3032278
X-RAY DIFFRACTIONf_dihedral_angle_d14.143646
X-RAY DIFFRACTIONf_chiral_restr0.079230
X-RAY DIFFRACTIONf_plane_restr0.008299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5499-1.59990.28041180.25212305X-RAY DIFFRACTION90
1.5999-1.65710.26851510.22082546X-RAY DIFFRACTION99
1.6571-1.72340.23191240.19292572X-RAY DIFFRACTION100
1.7234-1.80180.21091410.17832558X-RAY DIFFRACTION100
1.8018-1.89680.20581460.18122529X-RAY DIFFRACTION99
1.8968-2.01560.1971500.17082588X-RAY DIFFRACTION100
2.0156-2.17120.17541260.162572X-RAY DIFFRACTION100
2.1712-2.38970.17121380.14792557X-RAY DIFFRACTION99
2.3897-2.73520.18161500.15522597X-RAY DIFFRACTION100
2.7352-3.44530.18421270.1572639X-RAY DIFFRACTION100
3.4453-30.07890.16621360.16232714X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.3649 Å / Origin y: 9.5293 Å / Origin z: 38.7389 Å
111213212223313233
T0.0654 Å20.012 Å2-0.0096 Å2-0.0661 Å20.0013 Å2--0.0773 Å2
L0.4773 °20.0618 °2-0.0033 °2-1.4075 °21.1904 °2--2.0351 °2
S-0.0075 Å °0.0553 Å °-0.0185 Å °-0.0857 Å °-0.0325 Å °0.0693 Å °-0.0207 Å °-0.0589 Å °0.0435 Å °
Refinement TLS groupSelection details: all

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