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- PDB-4gmj: Structure of human NOT1 MIF4G domain co-crystallized with CAF1 -

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Basic information

Entry
Database: PDB / ID: 4gmj
TitleStructure of human NOT1 MIF4G domain co-crystallized with CAF1
Components(CCR4-NOT transcription complex subunit ...) x 2
KeywordsRNA BINDING PROTEIN / CCR4-NOT / mRNA DECAY / DEADENYLASE / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / regulation of tyrosine phosphorylation of STAT protein / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway ...positive regulation of cytoplasmic mRNA processing body assembly / regulation of tyrosine phosphorylation of STAT protein / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / 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 / deadenylation-dependent decapping of nuclear-transcribed mRNA / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / P-body assembly / 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 / negative regulation of type I interferon-mediated signaling pathway / intracellular non-membrane-bounded organelle / positive regulation of viral genome replication / nuclear estrogen receptor binding / P-body / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / defense response to virus / DNA-binding transcription factor binding / negative regulation of translation / molecular adaptor activity / nuclear body / nuclear speck / 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 / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 7
C: CCR4-NOT transcription complex subunit 1
D: CCR4-NOT transcription complex subunit 7
E: CCR4-NOT transcription complex subunit 1
F: CCR4-NOT transcription complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,79220
Polymers178,2156
Non-polymers57714
Water3,801211
1
A: CCR4-NOT transcription complex subunit 1
B: CCR4-NOT transcription complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6057
Polymers59,4052
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-45 kcal/mol
Surface area22300 Å2
MethodPISA
2
C: CCR4-NOT transcription complex subunit 1
D: CCR4-NOT transcription complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5816
Polymers59,4052
Non-polymers1764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-42 kcal/mol
Surface area21960 Å2
MethodPISA
3
E: CCR4-NOT transcription complex subunit 1
F: CCR4-NOT transcription complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6057
Polymers59,4052
Non-polymers2005
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-45 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.470, 101.740, 142.200
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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CCR4-NOT transcription complex subunit ... , 2 types, 6 molecules ACEBDF

#1: 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.: 3 / 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: Protein CCR4-NOT transcription complex subunit 7 / BTG1-binding factor 1 / CCR4-associated factor 1 / CAF-1


Mass: 32776.035 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAF1, CNOT7 / Plasmid: pNEA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: Q9UIV1

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Non-polymers , 4 types, 225 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.1M Tris-HCl, 16% PEG8000, 0.2M MgCl2, 0.2M AMSO4, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: 2.7→82.21 Å / Num. obs: 63214 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.096 / Net I/σ(I): 11
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.5 / Num. unique all: 9227 / Rsym value: 0.577 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D5R

2d5r


Resolution: 2.7→76.7 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3201 5.07 %RANDOM
Rwork0.214 ---
obs0.2153 63168 99.4 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.698 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.966 Å2-0 Å29.213 Å2
2--2.3018 Å20 Å2
3----10.2678 Å2
Refinement stepCycle: LAST / Resolution: 2.7→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11869 0 29 211 12109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612180
X-RAY DIFFRACTIONf_angle_d0.80616506
X-RAY DIFFRACTIONf_dihedral_angle_d14.7614513
X-RAY DIFFRACTIONf_chiral_restr0.0411812
X-RAY DIFFRACTIONf_plane_restr0.0032101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.74030.32271350.33162630100
2.7403-2.78310.3521440.3244257499
2.7831-2.82880.37691460.3049258199
2.8288-2.87750.30861420.2942257199
2.8775-2.92990.35131650.2807257299
2.9299-2.98620.34831430.27552549100
2.9862-3.04720.32731240.28142661100
3.0472-3.11340.30131400.26722588100
3.1134-3.18590.33281410.25452641100
3.1859-3.26550.2911430.24782574100
3.2655-3.35380.31351490.24722586100
3.3538-3.45250.26481350.2483260099
3.4525-3.56390.26591310.2213260099
3.5639-3.69130.2671250.2237258199
3.6913-3.83910.25681360.21132625100
3.8391-4.01380.25251370.19612625100
4.0138-4.22540.21611250.18272654100
4.2254-4.49010.18761370.1735258599
4.4901-4.83680.19691430.1655263499
4.8368-5.32340.19431470.172258999
5.3234-6.09350.24411440.20292631100
6.0935-7.6760.22321390.2049263999
7.676-76.73860.16441300.1606267798

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