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- PDB-5ona: Drosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1 -

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Basic information

Entry
Database: PDB / ID: 5ona
TitleDrosophila Bag-of-marbles CBM peptide bound to human CAF40-CNOT1
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 9
  • Protein bag-of-marbles
KeywordsGENE REGULATION / DEADENYLATION / CCR4-NOT / TRANSLATIONAL REPRESSION / TRANSLATION
Function / homology
Function and homology information


male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of cytoplasmic mRNA processing body assembly / positive regulation of protein deubiquitination ...male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of cytoplasmic mRNA processing body assembly / positive regulation of protein deubiquitination / cell competition in a multicellular organism / CCR4-NOT core complex / spermatogonial cell division / armadillo repeat domain binding / female germ-line stem cell asymmetric division / CCR4-NOT complex / 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 / germ-line stem cell population maintenance / gamete generation / sex differentiation / positive regulation of stem cell differentiation / 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 / positive regulation of protein K63-linked deubiquitination / positive regulation of smoothened signaling pathway / regulatory ncRNA-mediated gene silencing / 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 / epidermal growth factor receptor binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of epidermal growth factor receptor signaling pathway / oogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of peptidyl-serine phosphorylation / mRNA regulatory element binding translation repressor activity / ubiquitin binding / mRNA 3'-UTR binding / nuclear estrogen receptor binding / P-body / cytokine-mediated signaling pathway / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spermatogenesis / molecular adaptor activity / transcription coactivator activity / negative regulation of translation / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-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 9 / Cell differentiation family, Rcd1-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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / Protein bag of marbles / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRaisch, T. / Sgromo, A. / Backhaus, C. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: RNA / Year: 2018
Title: DrosophilaBag-of-marbles directly interacts with the CAF40 subunit of the CCR4-NOT complex to elicit repression of mRNA targets.
Authors: Sgromo, A. / Raisch, T. / Backhaus, C. / Keskeny, C. / Alva, V. / Weichenrieder, O. / Izaurralde, E.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 9
C: Protein bag-of-marbles
D: CCR4-NOT transcription complex subunit 1
E: CCR4-NOT transcription complex subunit 9
F: Protein bag-of-marbles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,25619
Polymers123,1286
Non-polymers1,12813
Water00
1
A: CCR4-NOT transcription complex subunit 1
B: CCR4-NOT transcription complex subunit 9
C: Protein bag-of-marbles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,40413
Polymers61,5643
Non-polymers83910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-151 kcal/mol
Surface area24340 Å2
MethodPISA
2
D: CCR4-NOT transcription complex subunit 1
E: CCR4-NOT transcription complex subunit 9
F: Protein bag-of-marbles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8526
Polymers61,5643
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-60 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.600, 106.600, 263.430
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
11A-1601-

SO4

21D-1601-

SO4

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Components

#1: Protein CCR4-NOT transcription complex subunit 1 / CCR4-associated factor 1 / Negative regulator of transcription subunit 1 homolog / hNOT1


Mass: 27617.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first 6 residues (GPHMLE) remain from the protease cleavage site and the linker.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT1, CDC39, KIAA1007, NOT1, AD-005 / Plasmid: PETMCN (PNYC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: A5YKK6
#2: Protein CCR4-NOT transcription complex subunit 9 / Cell differentiation protein RQCD1 homolog / Rcd-1


Mass: 31072.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first 6 residues (GPHMLE) remain from the protease cleavage site and the linker.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Plasmid: PETMCN (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600
#3: Protein/peptide Protein bag-of-marbles


Mass: 2874.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P22745
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.51 Å3/Da / Density % sol: 64.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 1.5 M ammonium sulfate 20 mM MES (pH 6.0) 80 mM MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS
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→50 Å / Num. obs: 48613 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 72.4 Å2 / Rsym value: 0.114 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3529 / Rsym value: 2.224 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CRU

4cru


Resolution: 2.7→49.408 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.27
RfactorNum. reflection% reflection
Rfree0.2373 2305 4.76 %
Rwork0.2088 --
obs0.2102 48454 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 97.9 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8424 0 57 0 8481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028628
X-RAY DIFFRACTIONf_angle_d0.43711694
X-RAY DIFFRACTIONf_dihedral_angle_d11.4175343
X-RAY DIFFRACTIONf_chiral_restr0.0361343
X-RAY DIFFRACTIONf_plane_restr0.0041505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.75890.42221680.38712806X-RAY DIFFRACTION99
2.7589-2.82310.35571180.34182862X-RAY DIFFRACTION99
2.8231-2.89370.34511260.31952850X-RAY DIFFRACTION99
2.8937-2.97190.38231840.29912794X-RAY DIFFRACTION100
2.9719-3.05940.31271540.28392821X-RAY DIFFRACTION100
3.0594-3.15810.32161100.28892859X-RAY DIFFRACTION100
3.1581-3.2710.34691370.2622848X-RAY DIFFRACTION100
3.271-3.40190.29831420.24262859X-RAY DIFFRACTION100
3.4019-3.55670.28071510.22512914X-RAY DIFFRACTION100
3.5567-3.74410.24531200.22112871X-RAY DIFFRACTION100
3.7441-3.97860.24441440.19842885X-RAY DIFFRACTION100
3.9786-4.28570.1831190.17752911X-RAY DIFFRACTION100
4.2857-4.71660.18971580.16892882X-RAY DIFFRACTION100
4.7166-5.39840.2091560.17642914X-RAY DIFFRACTION100
5.3984-6.79860.24241610.22172950X-RAY DIFFRACTION100
6.7986-49.41620.18391570.1693123X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.32711.6641.58231.83321.66221.5263-0.04220.2221-0.0393-0.1460.2073-0.1846-0.34490.236-0.17420.7057-0.17170.04060.60560.01420.572147.8829-17.8538-26.8417
21.4243-0.17560.36660.7579-0.11893.36410.0817-0.2793-0.00910.2096-0.04480.0534-0.08510.3494-0.03390.6266-0.210.03860.5169-0.00350.539436.9739-34.1725-7.9354
35.0491-1.63520.60617.2246-0.14884.20450.2495-0.9584-0.212-0.18080.05241.0251-0.3022-0.2886-0.36280.8643-0.21210.08710.8402-0.02240.753725.9586-25.6862-2.6467
43.50540.66820.28821.18780.7022.5346-0.1009-0.7387-0.15050.20350.0746-0.18290.21690.8512-0.0660.99280.08420.00781.390.02190.893261.7628-48.9136-23.3554
51.64340.2606-0.85522.0809-0.48911.32440.16130.1012-0.0091-0.3449-0.0216-0.225-0.18960.4504-0.12790.99760.03230.1151.2814-0.12570.848465.6717-35.662-47.0725
63.77680.83230.83521.5746-0.69894.8691-0.00450.8735-0.59470.2364-0.70980.09930.0051-0.38270.64361.17340.07620.11731.7334-0.28461.001773.2822-45.2728-54.9993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1353 through 1588)
2X-RAY DIFFRACTION2(chain 'B' and resid 13 through 285)
3X-RAY DIFFRACTION3(chain 'C' and resid 13 through 34)
4X-RAY DIFFRACTION4(chain 'D' and resid 1351 through 1588)
5X-RAY DIFFRACTION5(chain 'E' and resid 15 through 285)
6X-RAY DIFFRACTION6(chain 'F' and resid 14 through 34)

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