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- PDB-5anr: Structure of a human 4E-T - DDX6 - CNOT1 complex -

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Basic information

Entry
Database: PDB / ID: 5anr
TitleStructure of a human 4E-T - DDX6 - CNOT1 complex
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER
  • PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / armadillo repeat domain binding / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / mRNA decay by 5' to 3' exoribonuclease / negative regulation of intracellular estrogen receptor signaling pathway ...negative regulation of deadenylation-dependent decapping of nuclear-transcribed mRNA / positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / armadillo repeat domain binding / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / mRNA decay by 5' to 3' exoribonuclease / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / nuclear export signal receptor activity / miRNA-mediated post-transcriptional gene silencing / viral RNA genome packaging / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / RISC complex / mRNA stabilization / peroxisomal membrane / 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 / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / stem cell population maintenance / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of neuron differentiation / stress granule assembly / nuclear estrogen receptor binding / helicase activity / P-body / PML body / neuron differentiation / kinase binding / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / protein import into nucleus / molecular adaptor activity / RNA helicase activity / negative regulation of translation / RNA helicase / nuclear speck / cadherin binding / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular space / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / CCR4-NOT transcription complex subunit 1, N-terminal 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 ...Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / CCR4-NOT transcription complex subunit 1, N-terminal 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 / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / Probable ATP-dependent RNA helicase DDX6 / Eukaryotic translation initiation factor 4E transporter
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsBasquin, J. / Oezguer, S. / Conti, E.
CitationJournal: Cell Rep. / Year: 2015
Title: Structure of a Human 4E-T/Ddx6/Cnot1 Complex Reveals the Different Interplay of Ddx6-Binding Proteins with the Ccr4-not Complex.
Authors: Ozgur, S. / Basquin, J. / Kamenska, A. / Filipowicz, W. / Standart, N. / Conti, E.
History
DepositionSep 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

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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: PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER


Theoretical massNumber of molelcules
Total (without water)77,9773
Polymers77,9773
Non-polymers00
Water4,972276
1
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1

B: PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER


Theoretical massNumber of molelcules
Total (without water)77,9773
Polymers77,9773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_564-y,x-y+1,z-1/31
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-20.7 kcal/mol
Surface area29280 Å2
MethodPISA
2
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1

B: PROBABLE ATP-DEPENDENT RNA HELICASE DDX6
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER


Theoretical massNumber of molelcules
Total (without water)77,9773
Polymers77,9773
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x+y-1,-x,z+1/31
Buried area4020 Å2
ΔGint-20.7 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.129, 93.129, 175.329
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2133-

HOH

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Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CCR4-ASSOCIATED FACTOR 1 / NOT1H / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / HNOT1 / ...CCR4-ASSOCIATED FACTOR 1 / NOT1H / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / HNOT1 / CNOT1-MIF4G DOMAIN


Mass: 29695.352 Da / Num. of mol.: 1 / Fragment: MIF4G DOMAIN, UNP RESIDUES 1063-1314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: A5YKK6
#2: Protein PROBABLE ATP-DEPENDENT RNA HELICASE DDX6 / ATP-DEPENDENT RNA HELICASE P54 / DEAD BOX PROTEIN 6 / ONCOGENE RCK / DDX6


Mass: 43189.195 Da / Num. of mol.: 1 / Fragment: RECA1 AND RECA2, UNP RESIDUES 95-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P26196, RNA helicase
#3: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER / 4E-T / EIF4E TRANSPORTER / EUKARYOTIC TRANSLATION INITIATION FACTOR 4E NUCLEAR IMPORT FACTOR 1 / 4ET


Mass: 5092.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 199-239
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: Q9NRA8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A: QGPDSM IS COMING FROM THE CLEAVAGE SITE CHAIN B: RSM IS COMING FROM THE CLEAVAGE SITE ...CHAIN A: QGPDSM IS COMING FROM THE CLEAVAGE SITE CHAIN B: RSM IS COMING FROM THE CLEAVAGE SITE CHAIN C: RSM IS COMING FROM THE CLEAVAGE SITE

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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: 2.32 Å3/Da / Density % sol: 47.01 % / Description: NONE
Crystal growpH: 8 / Details: 50 MM TRIS PH 8.0, 35% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2014 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.32 Å / Num. obs: 51910 / % possible obs: 99.7 % / Observed criterion σ(I): 1.6 / Redundancy: 9.4 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.61
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CT4

4ct4


Resolution: 2.102→47.324 Å / SU ML: 0.25 / σ(F): 1.05 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 4923 5 %
Rwork0.1931 --
obs0.195 51865 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.102→47.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4929 0 0 276 5205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085008
X-RAY DIFFRACTIONf_angle_d1.0356784
X-RAY DIFFRACTIONf_dihedral_angle_d14.0071861
X-RAY DIFFRACTIONf_chiral_restr0.039801
X-RAY DIFFRACTIONf_plane_restr0.005865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1015-2.12540.43951450.37492814X-RAY DIFFRACTION89
2.1254-2.15040.36511630.34183069X-RAY DIFFRACTION99
2.1504-2.17660.32871650.31283145X-RAY DIFFRACTION98
2.1766-2.20420.32121640.29123102X-RAY DIFFRACTION100
2.2042-2.23320.29621590.29113090X-RAY DIFFRACTION99
2.2332-2.26380.32281680.27993146X-RAY DIFFRACTION99
2.2638-2.29610.32281620.27073107X-RAY DIFFRACTION100
2.2961-2.33040.26571630.25283167X-RAY DIFFRACTION100
2.3304-2.36680.28691630.23323119X-RAY DIFFRACTION100
2.3668-2.40560.3091660.23093121X-RAY DIFFRACTION100
2.4056-2.44710.24371670.20713159X-RAY DIFFRACTION100
2.4471-2.49160.24541620.21373107X-RAY DIFFRACTION100
2.4916-2.53950.3121680.22553165X-RAY DIFFRACTION100
2.5395-2.59130.22511630.21823136X-RAY DIFFRACTION100
2.5913-2.64770.27591650.20833161X-RAY DIFFRACTION100
2.6477-2.70920.22191670.20833114X-RAY DIFFRACTION100
2.7092-2.7770.26321630.20173118X-RAY DIFFRACTION100
2.777-2.85210.2511660.1983119X-RAY DIFFRACTION100
2.8521-2.9360.25091650.23167X-RAY DIFFRACTION100
2.936-3.03070.26761660.20153108X-RAY DIFFRACTION100
3.0307-3.1390.22971660.1993135X-RAY DIFFRACTION100
3.139-3.26470.22081600.19033121X-RAY DIFFRACTION100
3.2647-3.41320.22761630.18123154X-RAY DIFFRACTION100
3.4132-3.59310.22391690.16983143X-RAY DIFFRACTION100
3.5931-3.81810.22451650.17123149X-RAY DIFFRACTION100
3.8181-4.11280.20811660.16463124X-RAY DIFFRACTION100
4.1128-4.52640.1671650.15273126X-RAY DIFFRACTION100
4.5264-5.18060.20021680.16013154X-RAY DIFFRACTION100
5.1806-6.52430.22891680.20163109X-RAY DIFFRACTION100
6.5243-47.33630.1971630.15973156X-RAY DIFFRACTION100

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