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- PDB-4gml: Crystal structure of human NOT1 MIF4G domain -

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Basic information

Entry
Database: PDB / ID: 4gml
TitleCrystal structure of human NOT1 MIF4G domain
ComponentsCCR4-NOT transcription complex subunit 1
KeywordsRNA BINDING PROTEIN / CCR4-NOT / DEADENYLATION / mRNA DECAY / DEADENYLASE / 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 / 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 / nuclear estrogen receptor binding / P-body / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / membrane / nucleus / cytosol
Similarity search - Function
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 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPetit, P. / Weichenrieder, O. / Wohlbold, L. / Izaurralde, E.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex
Authors: Petit, A.P. / Wohlbold, L. / Bawankar, P. / Huntzinger, E. / Schmidt, S. / Izaurralde, E. / Weichenrieder, O.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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 1
C: CCR4-NOT transcription complex subunit 1
D: CCR4-NOT transcription complex subunit 1
E: CCR4-NOT transcription complex subunit 1
F: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)163,6246
Polymers163,6246
Non-polymers00
Water54030
1
A: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: CCR4-NOT transcription complex subunit 1


Theoretical massNumber of molelcules
Total (without water)27,2711
Polymers27,2711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.270, 133.823, 331.843
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 27270.738 Da / Num. of mol.: 6 / Fragment: NOT1 MIF4G domain, UNP residues 1093-1317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD-005, CDC39, CNOT1, KIAA1007, NOT1 / Plasmid: pNEA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Codon plus / References: UniProt: A5YKK6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M BTP, 1.6M AmSO4, 0.2M LiCl , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→49.31 Å / Num. all: 44111 / Num. obs: 44067 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.082 / Net I/σ(I): 17.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6363 / Rsym value: 0.716 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GMJ

4gmj


Resolution: 2.9→49.31 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 2216 5.04 %RANDOM
Rwork0.1899 ---
obs0.1918 43989 99.84 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.823 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-27.4797 Å2-0 Å2-0 Å2
2---5.5112 Å20 Å2
3----21.9684 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11102 0 0 30 11132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311318
X-RAY DIFFRACTIONf_angle_d0.70615340
X-RAY DIFFRACTIONf_dihedral_angle_d13.614240
X-RAY DIFFRACTIONf_chiral_restr0.051795
X-RAY DIFFRACTIONf_plane_restr0.0031948
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.96310.33341670.28152580100
2.9631-3.0320.35891210.2672570100
3.032-3.10780.29511360.23722574100
3.1078-3.19180.27311350.22072584100
3.1918-3.28570.2411260.20942590100
3.2857-3.39170.2691500.20762574100
3.3917-3.51290.25271340.19992608100
3.5129-3.65350.24321410.19462578100
3.6535-3.81980.20191310.17512633100
3.8198-4.02110.24441300.16932610100
4.0211-4.27290.20741300.16112585100
4.2729-4.60250.18951470.15572599100
4.6025-5.06530.18891380.1572624100
5.0653-5.79730.23181470.19892638100
5.7973-7.30010.25681490.23242668100
7.3001-49.3210.19031340.1796275899

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